1
|
Dunkelmann DL, Chin JW. Engineering Pyrrolysine Systems for Genetic Code Expansion and Reprogramming. Chem Rev 2024; 124:11008-11062. [PMID: 39235427 PMCID: PMC11467909 DOI: 10.1021/acs.chemrev.4c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
Over the past 16 years, genetic code expansion and reprogramming in living organisms has been transformed by advances that leverage the unique properties of pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs. Here we summarize the discovery of the pyrrolysine system and describe the unique properties of PylRS/tRNAPyl pairs that provide a foundation for their transformational role in genetic code expansion and reprogramming. We describe the development of genetic code expansion, from E. coli to all domains of life, using PylRS/tRNAPyl pairs, and the development of systems that biosynthesize and incorporate ncAAs using pyl systems. We review applications that have been uniquely enabled by the development of PylRS/tRNAPyl pairs for incorporating new noncanonical amino acids (ncAAs), and strategies for engineering PylRS/tRNAPyl pairs to add noncanonical monomers, beyond α-L-amino acids, to the genetic code of living organisms. We review rapid progress in the discovery and scalable generation of mutually orthogonal PylRS/tRNAPyl pairs that can be directed to incorporate diverse ncAAs in response to diverse codons, and we review strategies for incorporating multiple distinct ncAAs into proteins using mutually orthogonal PylRS/tRNAPyl pairs. Finally, we review recent advances in the encoded cellular synthesis of noncanonical polymers and macrocycles and discuss future developments for PylRS/tRNAPyl pairs.
Collapse
Affiliation(s)
- Daniel L. Dunkelmann
- Medical
Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
- Max
Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jason W. Chin
- Medical
Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
| |
Collapse
|
2
|
Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024; 124:10281-10362. [PMID: 39120726 PMCID: PMC11441406 DOI: 10.1021/acs.chemrev.3c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/10/2024] [Accepted: 06/27/2024] [Indexed: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
Collapse
Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A. Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
| |
Collapse
|
3
|
Zhang S, Tang Q, Zhang X, Chen X. Proximitomics by Reactive Species. ACS CENTRAL SCIENCE 2024; 10:1135-1147. [PMID: 38947200 PMCID: PMC11212136 DOI: 10.1021/acscentsci.4c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 07/02/2024]
Abstract
The proximitome is defined as the entire collection of biomolecules spatially in the proximity of a biomolecule of interest. More broadly, the concept of the proximitome can be extended to the totality of cells proximal to a specific cell type. Since the spatial organization of biomolecules and cells is essential for almost all biological processes, proximitomics has recently emerged as an active area of scientific research. One of the growing strategies for proximitomics leverages reactive species-which are generated in situ and spatially confined, to chemically tag and capture proximal biomolecules and cells for systematic analysis. In this Outlook, we summarize different types of reactive species that have been exploited for proximitomics and discuss their pros and cons for specific applications. In addition, we discuss the current challenges and future directions of this exciting field.
Collapse
Affiliation(s)
- Shaoran Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Qi Tang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
| | - Xu Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Xing Chen
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
- Synthetic
and Functional Biomolecules Center, Peking
University, Beijing 100871, People’s
Republic of China
- Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry
of Education, Peking University, Beijing 100871, People’s Republic of China
| |
Collapse
|
4
|
Liu DD, Ding W, Cheng JT, Wei Q, Lin Y, Zhu TY, Tian J, Sun K, Zhang L, Lu P, Yang F, Liu C, Tang S, Yang B. Characterize direct protein interactions with enrichable, cleavable and latent bioreactive unnatural amino acids. Nat Commun 2024; 15:5221. [PMID: 38890329 PMCID: PMC11189575 DOI: 10.1038/s41467-024-49517-1] [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: 01/28/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Latent bioreactive unnatural amino acids (Uaas) have been widely used in the development of covalent drugs and identification of protein interactors, such as proteins, DNA, RNA and carbohydrates. However, it is challenging to perform high-throughput identification of Uaa cross-linking products due to the complexities of protein samples and the data analysis processes. Enrichable Uaas can effectively reduce the complexities of protein samples and simplify data analysis, but few cross-linked peptides were identified from mammalian cell samples with these Uaas. Here we develop an enrichable and multiple amino acids reactive Uaa, eFSY, and demonstrate that eFSY is MS cleavable when eFSY-Lys and eFSY-His are the cross-linking products. An identification software, AixUaa is developed to decipher eFSY mass cleavable data. We systematically identify direct interactomes of Thioredoxin 1 (Trx1) and Selenoprotein M (SELM) with eFSY and AixUaa.
Collapse
Affiliation(s)
- Dan-Dan Liu
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wenlong Ding
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jin-Tao Cheng
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Qiushi Wei
- School of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Yinuo Lin
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China
| | - Tian-Yi Zhu
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jing Tian
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China
| | - Ke Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310030, China
| | - Long Zhang
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Peilong Lu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310030, China
| | - Fan Yang
- Department of Biophysics, Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Chao Liu
- School of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang University, Beijing, 100191, China.
| | - Shibing Tang
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China.
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, 510530, China.
| | - Bing Yang
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| |
Collapse
|
5
|
Ding W, Yu W, Chen Y, Lao L, Fang Y, Fang C, Zhao H, Yang B, Lin S. Rare codon recoding for efficient noncanonical amino acid incorporation in mammalian cells. Science 2024; 384:1134-1142. [PMID: 38843324 DOI: 10.1126/science.adm8143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/03/2024] [Indexed: 06/16/2024]
Abstract
The ability to genetically encode noncanonical amino acids (ncAAs) has empowered proteins with improved or previously unknown properties. However, existing strategies in mammalian cells rely on the introduction of a blank codon to incorporate ncAAs, which is inefficient and limits their widespread applications. In this study, we developed a rare codon recoding strategy that takes advantage of the relative rarity of the TCG codon to achieve highly selective and efficient ncAA incorporation through systematic engineering and big data-model predictions. We highlight the broad utility of this strategy for the incorporation of dozens of ncAAs into various functional proteins at the wild-type protein expression levels, as well as the synthesis of proteins with up to six-site ncAAs or four distinct ncAAs in mammalian cells for downstream applications.
Collapse
Affiliation(s)
- Wenlong Ding
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Wei Yu
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Yulin Chen
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Lihui Lao
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Yu Fang
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Chengzhu Fang
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Hongxia Zhao
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Bo Yang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Shixian Lin
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
- Department of Medical Oncology, State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| |
Collapse
|
6
|
Faustino AM, Sharma P, Manriquez-Sandoval E, Yadav D, Fried SD. Progress toward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization of Protein Structures and Networks In Vivo. Anal Chem 2023; 95:10670-10685. [PMID: 37341467 DOI: 10.1021/acs.analchem.3c01369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is emerging as a method at the crossroads of structural and cellular biology, uniquely capable of identifying protein-protein interactions with residue-level resolution and on the proteome-wide scale. With the development of cross-linkers that can form linkages inside cells and easily cleave during fragmentation on the mass spectrometer (MS-cleavable cross-links), it has become increasingly facile to identify contacts between any two proteins in complex samples, including in live cells or tissues. Photo-cross-linkers possess the advantages of high temporal resolution and high reactivity, thereby engaging all residue-types (rather than just lysine); nevertheless, photo-cross-linkers have not enjoyed widespread use and are yet to be employed for proteome-wide studies because their products are challenging to identify. Here, we demonstrate the synthesis and application of two heterobifunctional photo-cross-linkers that feature diazirines and N-hydroxy-succinimidyl carbamate groups, the latter of which unveil doubly fissile MS-cleavable linkages upon acyl transfer to protein targets. Moreover, these cross-linkers demonstrate high water-solubility and cell-permeability. Using these compounds, we demonstrate the feasibility of proteome-wide photo-cross-linking in cellulo. These studies elucidate a small portion of Escherichia coli's interaction network, albeit with residue-level resolution. With further optimization, these methods will enable the detection of protein quinary interaction networks in their native environment at residue-level resolution, and we expect that they will prove useful toward the effort to explore the molecular sociology of the cell.
Collapse
Affiliation(s)
- Anneliese M Faustino
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Piyoosh Sharma
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Edgar Manriquez-Sandoval
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Divya Yadav
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
7
|
Nadendla K, Simpson GG, Becher J, Journeaux T, Cabeza-Cabrerizo M, Bernardes GJL. Strategies for Conditional Regulation of Proteins. JACS AU 2023; 3:344-357. [PMID: 36873677 PMCID: PMC9975842 DOI: 10.1021/jacsau.2c00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Design of the next-generation of therapeutics, biosensors, and molecular tools for basic research requires that we bring protein activity under control. Each protein has unique properties, and therefore, it is critical to tailor the current techniques to develop new regulatory methods and regulate new proteins of interest (POIs). This perspective gives an overview of the widely used stimuli and synthetic and natural methods for conditional regulation of proteins.
Collapse
Affiliation(s)
- Karthik Nadendla
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CB2 1EW, Cambridge, U.K.
| | - Grant G. Simpson
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CB2 1EW, Cambridge, U.K.
| | - Julie Becher
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CB2 1EW, Cambridge, U.K.
| | - Toby Journeaux
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CB2 1EW, Cambridge, U.K.
| | - Mar Cabeza-Cabrerizo
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CB2 1EW, Cambridge, U.K.
| | - Gonçalo J. L. Bernardes
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CB2 1EW, Cambridge, U.K.
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| |
Collapse
|
8
|
Shu X, Liao QQ, Li ST, Liu L, Zhang X, Zhou L, Zhang L, Coin I, Wang L, Wu H, Yang B. Detecting Active Deconjugating Enzymes with Genetically Encoded Activity-Based Ubiquitin and Ubiquitin-like Protein Probes. Anal Chem 2023; 95:846-853. [PMID: 36595388 DOI: 10.1021/acs.analchem.2c03270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Post-translational modification of proteins by Ubiquitin (Ub) and Ubiquitin-like proteins (Ubls) can be reversed by deconjugating enzymes, which have been implicated in different pathways and associated with various human diseases. To understand the activity and dynamics of deconjugating enzymes, multiple synthetic and semi-synthetic Ub/Ubl probes have been developed, and some of them have been applied to screen inhibitors of deconjugating enzymes. Since these Ub/Ubl probes are generally not cell-permeable, different strategies have been developed to deliver Ub/Ubl probes to live cells. However, till now, no Ub/Ubl probes can be expressed in live cells to directly report on the activities of deconjugating enzymes in the most relevant cellular environment. Here, we genetically encoded cross-linkable Ub/Ubl probes in live E. coli and HEK293T cells. These probes can cross-link with deconjugating enzymes in vitro and in vivo. Using these Ub probes combined with mass spectrometry, we have successfully identified endogenous deconjugating enzymes in live cells. We believe that these genetically encoded Ub/Ubl probes are valuable for investigating biological functions of deconjugating enzymes in physiological environments.
Collapse
Affiliation(s)
- Xin Shu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qing-Qing Liao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shang-Tong Li
- Glbizzia Biosciences Company Limited, Beijing 102601, China
| | - Lu Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiajun Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lianqi Zhou
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Long Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig 04103, Germany
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158, United States
| | - Haifan Wu
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
9
|
Dorn RS, Prescher JA. Bioorthogonal Phosphines: Then and Now. Isr J Chem 2022. [DOI: 10.1002/ijch.202200070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Robert S. Dorn
- Departments of Chemistry University of California Irvine California 92697 United States
| | - Jennifer A. Prescher
- Departments of Chemistry University of California Irvine California 92697 United States
- Molecular Biology & Biochemistry University of California Irvine California 92697 United States
- Pharmaceutical Sciences University of California Irvine California 92697 United States
| |
Collapse
|
10
|
Apostolos AJ, Ocius KL, Koyasseril-Yehiya TM, Santamaria C, Silva JRA, Lameira J, Alves CN, Siegrist MS, Pires MM. Metabolic Processing of Selenium-Based Bioisosteres of meso-Diaminopimelic Acid in Live Bacteria. Biochemistry 2022; 61:1404-1414. [PMID: 35687722 DOI: 10.1021/acs.biochem.2c00120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A primary component of all known bacterial cell walls is the peptidoglycan (PG) layer, which is composed of repeating units of sugars connected to short and unusual peptides. The various steps within PG biosynthesis are targets of potent antibiotics as proper assembly of the PG is essential for cellular growth and survival. Synthetic mimics of PG have proven to be indispensable tools to study the bacterial cell structure, growth, and remodeling. Yet, a common component of PG, meso-diaminopimelic acid (m-DAP) at the third position of the stem peptide, remains challenging to access synthetically and is not commercially available. Here, we describe the synthesis and metabolic processing of a selenium-based bioisostere of m-DAP (selenolanthionine) and show that it is installed within the PG of live bacteria by the native cell wall crosslinking machinery in mycobacterial species. This PG probe has an orthogonal release mechanism that could be important for downstream proteomics studies. Finally, we describe a bead-based assay that is compatible with high-throughput screening of cell wall enzymes. We envision that this probe will supplement the current methods available for investigating PG crosslinking in m-DAP-containing organisms.
Collapse
Affiliation(s)
- Alexis J Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Karl L Ocius
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | | | - Carolina Santamaria
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States.,Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States
| | - José Rogério A Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Cláudio N Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - M Sloan Siegrist
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States.,Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| |
Collapse
|
11
|
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.
Collapse
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,
| |
Collapse
|
12
|
Wang S, Zhou Q, Li Y, Wei B, Liu X, Zhao J, Ye F, Zhou Z, Ding B, Wang P. Quinoline-Based Photolabile Protection Strategy Facilitates Efficient Protein Assembly. J Am Chem Soc 2022; 144:1232-1242. [PMID: 35034454 DOI: 10.1021/jacs.1c10324] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Native chemical ligation (NCL) provides a powerful solution to assemble proteins with precise chemical features, which enables a detailed investigation of the protein structure-function relationship. As an extension to NCL, the discovery of desulfurization and expressed protein ligation (EPL) techniques has greatly expanded the efficient access to large or challenging protein sequences via chemical ligations. Despite its superior reliability, the NCL-desulfurization protocol requires orthogonal protection strategies to allow selective desulfurization in the presence of native Cys, which is crucial to its synthetic application. In contrast to traditional thiol protecting groups, photolabile protecting groups (PPGs), which are removed upon irradiation, simplify protein assembly and therefore provide minimal perturbation to the peptide scaffold. However, current PPG strategies are mainly limited to nitro-benzyl derivatives, which are incompatible with NCL-desulfurization. Herein, we present for the first time that quinoline-based PPG for cysteine can facilitate various ligation strategies, including iterative NCL and EPL-desulfurization methods. 7-(Piperazin-1-yl)-2-(methyl)quinolinyl (PPZQ) caging of multiple cysteine residues within the protein sequence can be readily introduced via late-stage modification, while the traceless removal of PPZQ is highly efficient via photolysis in an aqueous buffer. In addition, the PPZQ group is compatible with radical desulfurization. The efficiency of this strategy has been highlighted by the synthesis of γ-synuclein and phosphorylated cystatin-S via one-pot iterative ligation and EPL-desulfurization methods. Besides, successful sextuple protection and deprotection of the expressed Interleukin-34 fragment demonstrate the great potential of this strategy in protein caging/uncaging investigations.
Collapse
Affiliation(s)
- Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qingqing Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yunxue Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Bingcheng Wei
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xinliang Liu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jie Zhao
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Farong Ye
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhongneng Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Bei Ding
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| |
Collapse
|
13
|
Dean Cho CC, Blankenship LR, Ma X, Xu S, Liu W. The Pyrrolysyl-tRNA Synthetase Activity can be Improved by a P188 Mutation that Stabilizes the Full-Length Enzyme. J Mol Biol 2022; 434:167453. [PMID: 35033561 PMCID: PMC9018550 DOI: 10.1016/j.jmb.2022.167453] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 12/18/2021] [Accepted: 01/09/2022] [Indexed: 11/24/2022]
Abstract
The amber suppression-based noncanonical amino acid (ncAA) mutagenesis technique has been widely used in both basic and applied research. So far more than two hundred ncAAs have been genetically encoded by amber codon in both prokaryotes and eukaryotes using wild-type and engineered pyrrolysyl-tRNA synthetase (PylRS)-tRNAPyl (PylT) pairs. Methanosarcina mazei PylRS (MmPylRS) is arguably one of two most used PylRS variants. However, it contains an unstable N-terminal domain that is usually cleaved from the full-length protein during expression and therefore leads to a low enzyme activity. We discovered that the cleavage takes place after A189 and this cleavage is inhibited when MmPylRS is co-expressed with Ca. Methanomethylophilus alvus tRNAPyl (CmaPylT). In the presence of CmaPylT, MmPylRS is cleaved after an alternative site K110. MmPylRS is active toward CmaPylT. Its combined use with CmaPylT leads to enhanced incorporation of Nε-Boc-lysine (BocK) at amber codon. To prevent MmPylRS from cleavage after A189 in the presence of its cognate M. mazei tRNAPyl (MmPylT), we introduced mutations at P188. Our results indicated that the P188G mutation stabilizes MmPylRS. We showed that the P188G mutation in wild-type MmPylRS or its engineered variants allows enhanced incorporation of BocK and other noncanonical amino acids including Nε-acetyl-lysine when they are co-expressed with MmPylT.
Collapse
Affiliation(s)
- Chia-Chuan Dean Cho
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Lauren R Blankenship
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Xinyu Ma
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Wenshe Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA.
| |
Collapse
|
14
|
Qiao Y, Yu G, Leeuwon SZ, Liu WR. Site-Specific Conversion of Cysteine in a Protein to Dehydroalanine Using 2-Nitro-5-thiocyanatobenzoic Acid. Molecules 2021; 26:2619. [PMID: 33947165 PMCID: PMC8125731 DOI: 10.3390/molecules26092619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 01/21/2023] Open
Abstract
Dehydroalanine exists natively in certain proteins and can also be chemically made from the protein cysteine. As a strong Michael acceptor, dehydroalanine in proteins has been explored to undergo reactions with different thiolate reagents for making close analogues of post-translational modifications (PTMs), including a variety of lysine PTMs. The chemical reagent 2-nitro-5-thiocyanatobenzoic acid (NTCB) selectively modifies cysteine to form S-cyano-cysteine, in which the S-Cβ bond is highly polarized. We explored the labile nature of this bond for triggering E2 elimination to generate dehydroalanine. Our results indicated that when cysteine is at the flexible C-terminal end of a protein, the dehydroalanine formation is highly effective. We produced ubiquitin and ubiquitin-like proteins with a C-terminal dehydroalanine residue with high yields. When cysteine is located at an internal region of a protein, the efficiency of the reaction varies with mainly hydrolysis products observed. Dehydroalanine in proteins such as ubiquitin and ubiquitin-like proteins can serve as probes for studying pathways involving ubiquitin and ubiquitin-like proteins and it is also a starting point to generate proteins with many PTM analogues; therefore, we believe that this NTCB-triggered dehydroalanine formation method will find broad applications in studying ubiquitin and ubiquitin-like protein pathways and the functional annotation of many PTMs in proteins such as histones.
Collapse
Affiliation(s)
- Yuchen Qiao
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.Q.); (G.Y.); (S.Z.L.)
| | - Ge Yu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.Q.); (G.Y.); (S.Z.L.)
| | - Sunshine Z. Leeuwon
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.Q.); (G.Y.); (S.Z.L.)
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.Q.); (G.Y.); (S.Z.L.)
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
- Molecular & Cellular Medicine Department, College of Medicine, Texas A&M University, College Station, TX 77843, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Beard HA, Korovesis D, Chen S, Verhelst SHL. Cleavable linkers and their application in MS-based target identification. Mol Omics 2021; 17:197-209. [PMID: 33507200 DOI: 10.1039/d0mo00181c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covalent chemical probes are important tools in chemical biology. They range from post-translational modification (PTM)-derived metabolic probes, to activity-based probes and photoaffinity labels. Identification of the probe targets is often performed by tandem mass spectrometry-based proteomics methods. In the past fifteen years, cleavable linker technologies have been implemented in these workflows in order to identify probe targets with lower background and higher confidence. In addition, the linkers have enabled identification of modification sites. Overall, this has led to an increased knowledge of PTMs, enzyme function and drug action. This review gives an overview of the different types of cleavable linkers, and their benefits and limitations. Their applicability in target identification is also illustrated by several specific examples.
Collapse
Affiliation(s)
- Hester A Beard
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49 box 802, 3000 Leuven, Belgium.
| | | | | | | |
Collapse
|
17
|
Chen C, Peng T. Protocol for Site-Specific Photo-Crosslinking Proteomics to Identify Protein-Protein Interactions in Mammalian Cells. STAR Protoc 2020; 1:100109. [PMID: 33377005 PMCID: PMC7756934 DOI: 10.1016/j.xpro.2020.100109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein-protein interactions (PPIs) play essential roles in almost all aspects of cellular processes. However, PPIs remain challenging to study due to their substoichiometry, low affinity, dynamic nature, and context dependence. Here, we present a protocol for the capture and identification of PPIs in live mammalian cells, which relies on site-specific photo-crosslinking in live cells, affinity purification, and quantitative proteomics. The protocol facilitates efficient and reliable identification of the interacting proteins of a given protein of interest in live cells. For complete details on the use and execution of this protocol, please refer to Wu et al. (2020).
Collapse
Affiliation(s)
- Chengjie Chen
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tao Peng
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Corresponding author
| |
Collapse
|
18
|
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
| |
Collapse
|
19
|
Jiang HK, Wang YH, Weng JH, Kurkute P, Li CL, Lee MN, Chen PJ, Tseng HW, Tsai MD, Wang YS. Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues. Biochemistry 2020; 59:2205-2209. [PMID: 32484330 DOI: 10.1021/acs.biochem.0c00307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA have been evolved to generate genetically encoded noncanonical amino acids (ncAAs). Use of tryptophan (Trp) analogues with pyrrole ring modification for their spatial and polarity tuning in enzyme activity and substrate specificity is still limited. Herein, we report the application of an evolved PylRS, FOWRS2, for efficient incorporation of five Trp analogues into the deubiquitinase USP30 to decipher the role of W475 for diubiquitin selectivity. Structures of the five FOWRS-C/Trp analogue complexes at 1.7-2.5 Å resolution showed multiple ncAA binding modes. The W475 near the USP30 active site was replaced with Trp analogues, and the effect on the activity as well as the selectivity toward diubiquitin linkage types was examined. It was found that the Trp analogue with a formyl group attached to the nitrogen atom of the indole ring led to an improved activity of USP30 likely due to enhanced polar interactions and that another Trp analogue, 3-benzothienyl-l-alanine, induced a unique K6-specificity. Collectively, genetically encoded noncanonical Trp analogues by evolved PylRS·tRNACUAPyl pair unravel the spatial role of USP30-W475 in its diubiquitin selectivity.
Collapse
Affiliation(s)
- Han-Kai Jiang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Yi-Hui Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Prashant Kurkute
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Chien-Lung Li
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Man-Nee Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Pei-Jung Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Hsueh-Wei Tseng
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yane-Shih Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
20
|
Genetically encoded protein labeling and crosslinking in living Pseudomonas aeruginosa. Bioorg Med Chem 2020; 28:115545. [PMID: 32503693 DOI: 10.1016/j.bmc.2020.115545] [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: 02/20/2020] [Revised: 04/18/2020] [Accepted: 04/30/2020] [Indexed: 01/06/2023]
Abstract
Pseudomonas aeruginosa (PA) is a major human pathogen for hospital-acquired infections. We report the genetic code expansion of this opportunistic pathogen by using the pyrrolysyl-tRNA synthetase-tRNA system, which enabled the genetic and site-specific incorporation of unnatural amino acids bearing bioorthogonal handles or photo-affinity groups into proteins in PA. This strategy allowed us to conduct bioorthogonal labeling and imaging of flagella, as well as site-specific photo-affinity capturing of interactions between a Type III secretion effector and its chaperone inside living bacteria.
Collapse
|
21
|
Bifunctional Non-Canonical Amino Acids: Combining Photo-Crosslinking with Click Chemistry. Biomolecules 2020; 10:biom10040578. [PMID: 32290035 PMCID: PMC7226127 DOI: 10.3390/biom10040578] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/04/2020] [Accepted: 04/05/2020] [Indexed: 12/27/2022] Open
Abstract
Genetic code expansion is a powerful tool for the study of protein interactions, as it allows for the site-specific incorporation of a photoreactive group via non-canonical amino acids. Recently, several groups have published bifunctional amino acids that carry a handle for click chemistry in addition to the photo-crosslinker. This allows for the specific labeling of crosslinked proteins and therefore the pulldown of peptides for further analysis. This review describes the properties and advantages of different bifunctional amino acids, and gives an overview about current and future applications.
Collapse
|
22
|
Wang C, Liu Y, Bao C, Xue Y, Zhou Y, Zhang D, Lin Q, Zhu L. Phototriggered labeling and crosslinking by 2-nitrobenzyl alcohol derivatives with amine selectivity. Chem Commun (Camb) 2020; 56:2264-2267. [PMID: 31984385 DOI: 10.1039/c9cc09449k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here we report the use of 2-nitrobenzyl alcohol (NB) as a photoreactive group with amine selectivity and explore its applications for photoaffinity labeling and crosslinking of biomolecules. This work confirms that NB is an efficient photoreactive group and has great potential in drug discovery, chemical biology and protein engineering.
Collapse
Affiliation(s)
- Chenxi Wang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Yuan Liu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Chunyan Bao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Yuan Xue
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Yaowu Zhou
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Dasheng Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Qiuning Lin
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Linyong Zhu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| |
Collapse
|
23
|
Mishra PK, Yoo CM, Hong E, Rhee HW. Photo-crosslinking: An Emerging Chemical Tool for Investigating Molecular Networks in Live Cells. Chembiochem 2020; 21:924-932. [PMID: 31794116 DOI: 10.1002/cbic.201900600] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/03/2019] [Indexed: 12/13/2022]
Abstract
Studying protein-protein interactions (PPIs) is useful for understanding cellular functions and mechanisms. Evaluating these PPIs under conditions as similar as possible to native conditions can be achieved using photo-crosslinking methods because of their on-demand ability to generate reactive species in situ by irradiation with UV light. Various fusion tag, metabolic incorporation, and amber codon suppression approaches using various crosslinkers containing aryl azide, benzophenone, and diazirines have been applied in live cells. Mass spectrometry and immunological techniques are used to identify crosslinked proteins based on their capture transient and context-dependent interactions. Herein we discuss various incorporation methods and crosslinkers that have been used for interactome mapping in live cells.
Collapse
Affiliation(s)
- Pratyush Kumar Mishra
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.,Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Chang-Mo Yoo
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eunmi Hong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 360-4 Dongnae-dong, Dong-gu, Daegu, 41061, Republic of Korea
| | - Hyun Woo Rhee
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| |
Collapse
|
24
|
Yang T, Li X, Li XD. A bifunctional amino acid to study protein–protein interactions. RSC Adv 2020; 10:42076-42083. [PMID: 35516754 PMCID: PMC9057919 DOI: 10.1039/d0ra09110c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/12/2020] [Indexed: 12/14/2022] Open
Abstract
dzANA is a novel bifunctional (photo-reactive and bioorthogonal) amino acid to study protein–protein interactions.
Collapse
Affiliation(s)
- Tangpo Yang
- Department of Chemistry
- The University of Hong Kong
- China
| | - Xin Li
- Department of Chemistry
- The University of Hong Kong
- China
| | | |
Collapse
|
25
|
Mapping low-affinity/high-specificity peptide-protein interactions using ligand-footprinting mass spectrometry. Proc Natl Acad Sci U S A 2019; 116:21001-21011. [PMID: 31578253 DOI: 10.1073/pnas.1819533116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Short linear peptide motifs that are intracellular ligands of folded proteins are a modular, incompletely understood molecular interaction language in signaling systems. Such motifs, which frequently occur in intrinsically disordered protein regions, often bind partner proteins with modest affinity and are difficult to study with conventional structural biology methods. We developed LiF-MS (ligand-footprinting mass spectrometry), a method to map peptide binding sites on folded protein domains that allows consideration of their dynamic disorder, and used it to analyze a set of D-motif peptide-mitogen-activated protein kinase (MAPK) associations to validate the approach and define unknown binding structures. LiF-MS peptide ligands carry a short-lived, indiscriminately reactive cleavable crosslinker that marks contacts close to ligand binding sites with high specificity. Each marked amino acid provides an independent constraint for a set of directed peptide-protein docking simulations, which are analyzed by agglomerative hierarchical clustering. We found that LiF-MS provides accurate ab initio identification of ligand binding surfaces and a view of potential binding ensembles of a set of D-motif peptide-MAPK associations. Our analysis provides an MKK4-JNK1 structural model, which has thus far been crystallographically unattainable, a potential alternate binding mode for part of the NFAT4-JNK interaction, and evidence of bidirectional association of MKK4 peptide with ERK2. Overall, we find that LiF-MS is an effective noncrystallographic way to understand how short linear motifs associate with specific sites on folded protein domains at the level of individual amino acids.
Collapse
|
26
|
Fu X, Chang Z. Biogenesis, quality control, and structural dynamics of proteins as explored in living cells via site-directed photocrosslinking. Protein Sci 2019; 28:1194-1209. [PMID: 31002747 DOI: 10.1002/pro.3627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/16/2019] [Indexed: 02/06/2023]
Abstract
Protein biogenesis and quality control are essential to maintaining a functional pool of proteins and involve numerous protein factors that dynamically and transiently interact with each other and with the substrate proteins in living cells. Conventional methods are hardly effective for studying dynamic, transient, and weak protein-protein interactions that occur in cells. Herein, we review how the site-directed photocrosslinking approach, which relies on the genetic incorporation of a photoreactive unnatural amino acid into a protein of interest at selected individual amino acid residue positions and the covalent trapping of the interacting proteins upon ultraviolent irradiation, has become a highly efficient way to explore the aspects of protein contacts in living cells. For example, in the past decade, this approach has allowed the profiling of the in vivo substrate proteins of chaperones or proteases under both physiologically optimal and stressful (e.g., acidic) conditions, mapping residues located at protein interfaces, identifying new protein factors involved in the biogenesis of membrane proteins, trapping transiently formed protein complexes, and snapshotting different structural states of a protein. We anticipate that the site-directed photocrosslinking approach will play a fundamental role in dissecting the detailed mechanisms of protein biogenesis, quality control, and dynamics in the future.
Collapse
Affiliation(s)
- Xinmiao Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province, 350117, China
| | - Zengyi Chang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Center for Protein Science, Beijing, 100871, China
| |
Collapse
|
27
|
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: 74] [Impact Index Per Article: 12.3] [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.
Collapse
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
| |
Collapse
|
28
|
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
| |
Collapse
|
29
|
Gao J, Yang F, Che J, Han Y, Wang Y, Chen N, Bak DW, Lai S, Xie X, Weerapana E, Wang C. Selenium-Encoded Isotopic Signature Targeted Profiling. ACS CENTRAL SCIENCE 2018; 4:960-970. [PMID: 30159393 PMCID: PMC6107865 DOI: 10.1021/acscentsci.8b00112] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Indexed: 05/09/2023]
Abstract
Selenium (Se), as an essential trace element, plays crucial roles in many organisms including humans. The biological functions of selenium are mainly mediated by selenoproteins, a unique class of selenium-containing proteins in which selenium is inserted in the form of selenocysteine. Due to their low abundance and uneven tissue distribution, detection of selenoproteins within proteomes is very challenging, and therefore functional studies of these proteins are limited. In this study, we developed a computational method, named as selenium-encoded isotopic signature targeted profiling (SESTAR), which utilizes the distinct natural isotopic distribution of selenium to assist detection of trace selenium-containing signals from shotgun-proteomic data. SESTAR can detect femtomole quantities of synthetic selenopeptides in a benchmark test and dramatically improved detection of native selenoproteins from tissue proteomes in a targeted profiling mode. By applying SESTAR to screen publicly available datasets from Human Proteome Map, we provide a comprehensive picture of selenoprotein distributions in human primary hematopoietic cells and tissues. We further demonstrated that SESTAR can aid chemical-proteomic strategies to identify additional selenoprotein targets of RSL3, a canonical inducer of cell ferroptosis. We believe SESTAR not only serves as a powerful tool for global profiling of native selenoproteomes, but can also work seamlessly with chemical-proteomic profiling strategies to enhance identification of target proteins, post-translational modifications, or protein-protein interactions.
Collapse
Affiliation(s)
- Jinjun Gao
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Peking−Tsinghua
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Fan Yang
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Jinteng Che
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Yu Han
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Yankun Wang
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Peking−Tsinghua
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Nan Chen
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Daniel W. Bak
- Department
of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Shuchang Lai
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao Xie
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Eranthie Weerapana
- Department
of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Chu Wang
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Peking−Tsinghua
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- E-mail:
| |
Collapse
|
30
|
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: 47] [Impact Index Per Article: 7.8] [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.
Collapse
Affiliation(s)
- Irene Coin
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04301 Leipzig, Germany.
| |
Collapse
|
31
|
Epigenetic chromatin modification by amber suppression technology. Curr Opin Chem Biol 2018; 45:1-9. [DOI: 10.1016/j.cbpa.2018.01.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/11/2018] [Accepted: 01/28/2018] [Indexed: 01/10/2023]
|
32
|
Tian Y, Lin Q. Genetic encoding of 2-aryl-5-carboxytetrazole-based protein photo-cross-linkers. Chem Commun (Camb) 2018; 54:4449-4452. [PMID: 29652063 DOI: 10.1039/c8cc02431f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Three γ-heteroatom-substituted N-methylpyrroletetrazole-lysines (mPyTXKs) were synthesized and subsequently incorporated into proteins site-specifically via genetic code expansion. The γ-seleno-substituted derivative, mPyTSeK, showed excellent incorporation efficiency in Escherichia coli and allowed site-selective photo-cross-linking of the GST dimer. Furthermore, the mPyTSeK-cross-linked GST dimer can be cleaved under mild oxidative conditions. The incorporation of mPyTXKs into proteins in mammalian cells was also demonstrated. Lastly, the recombinantly expressed mPyTSeK-encoded Grb2 was shown to covalently capture its interaction partner, EGFR, in mammalian cell lysate, which was subsequently released after treatment with H2O2.
Collapse
Affiliation(s)
- Yulin Tian
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, USA.
| | | |
Collapse
|
33
|
Abstract
Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.
Collapse
Affiliation(s)
- Douglas D. Young
- Department of Chemistry, College of William & Mary,
P.O. Box 8795, Williamsburg, VA 23187 (USA)
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute,
La Jolla, CA 92037 (USA),
| |
Collapse
|
34
|
He D, Xie X, Yang F, Zhang H, Su H, Ge Y, Song H, Chen PR. Quantitative and Comparative Profiling of Protease Substrates through a Genetically Encoded Multifunctional Photocrosslinker. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Dan He
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Xiao Xie
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Fan Yang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Heng Zhang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haomiao Su
- College of Chemistry and Molecular Sciences; Wuhan University; Wuhan 430072 China
| | - Yun Ge
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haiping Song
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Peng R. Chen
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| |
Collapse
|
35
|
He D, Xie X, Yang F, Zhang H, Su H, Ge Y, Song H, Chen PR. Quantitative and Comparative Profiling of Protease Substrates through a Genetically Encoded Multifunctional Photocrosslinker. Angew Chem Int Ed Engl 2017; 56:14521-14525. [DOI: 10.1002/anie.201708151] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/14/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Dan He
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Xiao Xie
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Fan Yang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Heng Zhang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haomiao Su
- College of Chemistry and Molecular Sciences; Wuhan University; Wuhan 430072 China
| | - Yun Ge
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haiping Song
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Peng R. Chen
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| |
Collapse
|
36
|
Yang Y, Song H, He D, Zhang S, Dai S, Xie X, Lin S, Hao Z, Zheng H, Chen PR. Genetically encoded releasable photo-cross-linking strategies for studying protein–protein interactions in living cells. Nat Protoc 2017; 12:2147-2168. [DOI: 10.1038/nprot.2017.090] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
37
|
Murale DP, Hong SC, Haque MM, Lee JS. Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs). Proteome Sci 2017; 15:14. [PMID: 28652856 PMCID: PMC5483283 DOI: 10.1186/s12953-017-0123-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/15/2017] [Indexed: 12/14/2022] Open
Abstract
Protein-protein interactions (PPIs) trigger a wide range of biological signaling pathways that are crucial for biomedical research and drug discovery. Various techniques have been used to study specific proteins, including affinity chromatography, activity-based probes, affinity-based probes and photo-affinity labeling (PAL). PAL has become one of the most powerful strategies to study PPIs. Traditional photocrosslinkers are used in PAL, including benzophenone, aryl azide, and diazirine. Upon photoirradiation, these photocrosslinkers (Pls) generate highly reactive species that react with adjacent molecules, resulting in a direct covalent modification. This review introduces recent examples of chemical proteomics study using PAL for PPIs.
Collapse
Affiliation(s)
- Dhiraj P Murale
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Seong Cheol Hong
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea.,Department of Biological Chemistry, KIST-School UST, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Md Mamunul Haque
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea.,Department of Biological Chemistry, KIST-School UST, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| |
Collapse
|
38
|
Zhang S, He D, Lin Z, Yang Y, Song H, Chen PR. Conditional Chaperone-Client Interactions Revealed by Genetically Encoded Photo-cross-linkers. Acc Chem Res 2017; 50:1184-1192. [PMID: 28467057 DOI: 10.1021/acs.accounts.6b00647] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The cell envelope is an integral and essential component of Gram-negative bacteria. As the front line during host-pathogen interactions, it is directly challenged by host immune responses as well as other harsh extracellular stimuli. The high permeability of the outer-membrane and the lack of ATP energy system render it difficult to maintain important biological activities within the periplasmic space under stress conditions. The HdeA/B chaperone machinery is the only known acid resistant system found in bacterial periplasm, enabling enteric pathogens to survive through the highly acidic human stomach and establish infections in the intestine. These two homologous chaperones belong to a fast growing family of conditionally disordered chaperones that conditionally lose their well-defined three-dimensional structures to exert biological activities. Upon losing ordered structures, these proteins commit promiscuous binding of diverse clients in response to environmental stimulation. For example, HdeA and HdeB are well-folded inactive dimers at neutral pH but become partially unfolded to protect a wide array of acid-denatured proteins upon acid stress. Whether these conditionally disordered chaperones possess client specificities remains unclear. This is in part due to the lack of efficient tools to investigate such versatile and heterogeneous protein-protein interactions under living conditions. Genetically encoded protein photo-cross-linkers have offered a powerful strategy to capture protein-protein interactions, showing great potential in profiling protein interaction networks, mapping binding interfaces, and probing dynamic changes in both physiological and pathological settings. Despite great success, photo-cross-linkers that can simultaneously capture the promiscuous binding partners and directly identify the interaction interfaces remain technically challenging. Furthermore, methods for side-by-side profiling and comparing the condition-dependent client pools from two homologous chaperones are lacking. Herein, we introduce our recent efforts in developing a panel of versatile genetically encoded photo-cross-linkers to study the disorder-mediated chaperone-client interactions in living cells. In particular, we have developed a series of proteomic-based strategies relying on these new photo-cross-linkers to systematically compare the client profiles of HdeA and HdeB, as well as to map their interaction interfaces. These studies revealed the mode-of-action, particularly the client specificity, of these two conditionally disordered chaperones. In the end, some recent elegant work from other groups that applied the genetically encoded photo-cross-linking strategy to illuminate important protein-protein interactions within bacterial cell envelope is also discussed.
Collapse
Affiliation(s)
- Shuai Zhang
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dan He
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhi Lin
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Yang
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Haiping Song
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peng R. Chen
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| |
Collapse
|
39
|
Tian Y, Jacinto MP, Zeng Y, Yu Z, Qu J, Liu WR, Lin Q. Genetically Encoded 2-Aryl-5-carboxytetrazoles for Site-Selective Protein Photo-Cross-Linking. J Am Chem Soc 2017; 139:6078-6081. [PMID: 28422494 PMCID: PMC5423124 DOI: 10.1021/jacs.7b02615] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The genetically encoded photo-cross-linkers promise to offer a temporally
controlled tool to map transient and dynamic protein–protein
interaction complexes in living cells. Here we report the synthesis
of a panel of 2-aryl-5-carboxytetrazole-lysine analogs (ACTKs) and
their site-specific incorporation into proteins via amber codon suppression
in Escherichia coli and mammalian cells.
Among five ACTKs investigated, N-methylpyrroletetrazole-lysine
(mPyTK) was found to give robust and site-selective photo-cross-linking
reactivity in E. coli when placed at
an appropriate site at the protein interaction interface. A comparison
study indicated that mPyTK exhibits higher photo-cross-linking efficiency
than a diazirine-based photo-cross-linker, AbK, when placed at the
same location of the interaction interface in vitro. When mPyTK was
introduced into the adapter protein Grb2, it enabled the photocapture
of EGFR in a stimulus-dependent manner. The design of mPyTK along
with the identification of its cognate aminoacyl-tRNA synthetase makes
it possible to map transient protein–protein interactions and
their interfaces in living cells.
Collapse
Affiliation(s)
- Yulin Tian
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260, United States
| | - Marco Paolo Jacinto
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260, United States
| | - Yu Zeng
- Department of Chemistry, Texas A&M University , College Station, Texas 77845, United States
| | - Zhipeng Yu
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo , Buffalo, New York 14260, United States
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University , College Station, Texas 77845, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260, United States
| |
Collapse
|
40
|
Lin Z, Xie X, Chen PR. Kicking down the ladder: adding cleavable features to genetically encoded photocrosslinkers. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0452-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
41
|
Ge Y, Fan X, Chen PR. A genetically encoded multifunctional unnatural amino acid for versatile protein manipulations in living cells. Chem Sci 2016; 7:7055-7060. [PMID: 28451140 PMCID: PMC5355830 DOI: 10.1039/c6sc02615j] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/01/2016] [Indexed: 01/20/2023] Open
Abstract
The genetic code expansion strategy allowed incorporation of unnatural amino acids (UAAs) bearing diverse functional groups into proteins, providing a powerful toolkit for protein manipulation in living cells. We report a multifunctional UAA, Nε-p-azidobenzyloxycarbonyl lysine (PABK), that possesses a panel of unique properties capable of fulfilling various protein manipulation purposes. In addition to being used as a bioorthogonal ligation handle, an infrared probe and a photo-affinity reagent, PABK was shown to be chemically decaged by trans-cyclooctenols via a strain-promoted 1,3-dipolar cycloaddition, which provides a new bioorthogonal cleavage strategy for intracellular protein activation. The biocompatibility and efficiency of this method were demonstrated by decaging of a PABK-caged firefly luciferase under living conditions. We further extended this method to chemically rescue a bacterial toxin OspF inside mammalian host cells.
Collapse
Affiliation(s)
- Yun Ge
- Beijing National Laboratory for Molecular Sciences , Synthetic and Functional Biomolecules Center , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Xinyuan Fan
- Beijing National Laboratory for Molecular Sciences , Synthetic and Functional Biomolecules Center , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
- Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China
| | - Peng R Chen
- Beijing National Laboratory for Molecular Sciences , Synthetic and Functional Biomolecules Center , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
- Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China
| |
Collapse
|
42
|
Yang Y, Song H, Chen PR. Genetically encoded photocrosslinkers for identifying and mapping protein-protein interactions in living cells. IUBMB Life 2016; 68:879-886. [DOI: 10.1002/iub.1560] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 09/03/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Yi Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University; Beijing China
| | - Haiping Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University; Beijing China
| | - Peng R. Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University; Beijing China
- Peking-Tsinghua Center for Life Sciences; Beijing China
| |
Collapse
|
43
|
Comparative proteomics reveal distinct chaperone-client interactions in supporting bacterial acid resistance. Proc Natl Acad Sci U S A 2016; 113:10872-7. [PMID: 27621474 DOI: 10.1073/pnas.1606360113] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
HdeA and HdeB constitute the essential chaperone system that functions in the unique periplasmic space of Gram-negative enteric bacteria to confer acid resistance. How this two-chaperone machinery cooperates to protect a broad range of client proteins from acid denaturation while avoiding nonspecific binding during bacterial passage through the highly acidic human stomach remains unclear. We have developed a comparative proteomic strategy that combines the genetically encoded releasable protein photocross-linker with 2D difference gel electrophoresis, which allows an unbiased side-by-side comparison of the entire client pools from these two acid-activated chaperones in Escherichia coli Our results reveal distinct client specificities between HdeA and HdeB in vivo that are determined mainly by their different responses to pH stimulus. The intracellular acidity serves as an environmental cue to determine the folding status of both chaperones and their clients, enabling specific chaperone-client binding and release under defined pH conditions. This cooperative and synergistic mode of action provides an efficient, economical, flexible, and finely tuned protein quality control strategy for coping with acid stress.
Collapse
|
44
|
Yang Y, Song H, He D, Zhang S, Dai S, Lin S, Meng R, Wang C, Chen PR. Genetically encoded protein photocrosslinker with a transferable mass spectrometry-identifiable label. Nat Commun 2016; 7:12299. [PMID: 27460181 PMCID: PMC4974458 DOI: 10.1038/ncomms12299] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 06/16/2016] [Indexed: 11/10/2022] Open
Abstract
Coupling photocrosslinking reagents with mass spectrometry has become a powerful tool for studying protein–protein interactions in living systems, but it still suffers from high rates of false-positive identifications as well as the lack of information on interaction interface due to the challenges in deciphering crosslinking peptides. Here we develop a genetically encoded photo-affinity unnatural amino acid that introduces a mass spectrometry-identifiable label (MS-label) to the captured prey proteins after photocrosslinking and prey–bait separation. This strategy, termed IMAPP (In-situ cleavage and MS-label transfer After Protein Photocrosslinking), enables direct identification of photo-captured substrate peptides that are difficult to uncover by conventional genetically encoded photocrosslinkers. Taking advantage of the MS-label, the IMAPP strategy significantly enhances the confidence for identifying protein–protein interactions and enables simultaneous mapping of the binding interface under living conditions. Mapping protein-protein interaction using crosslinking and mass spectroscopy strategies is hampered by a high rate of false-positive results. Here, the authors develop a genetically encoded photo-affinity probe for accurate identification of protein interaction partners and crosslinking sites.
Collapse
Affiliation(s)
- Yi Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Haiping Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dan He
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shuai Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shizhong Dai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shixian Lin
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Rong Meng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| |
Collapse
|
45
|
Itri F, Monti DM, Della Ventura B, Vinciguerra R, Chino M, Gesuele F, Lombardi A, Velotta R, Altucci C, Birolo L, Piccoli R, Arciello A. Femtosecond UV-laser pulses to unveil protein-protein interactions in living cells. Cell Mol Life Sci 2016; 73:637-48. [PMID: 26265182 PMCID: PMC11108384 DOI: 10.1007/s00018-015-2015-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/30/2015] [Accepted: 08/06/2015] [Indexed: 12/30/2022]
Abstract
A hallmark to decipher bioprocesses is to characterize protein-protein interactions in living cells. To do this, the development of innovative methodologies, which do not alter proteins and their natural environment, is particularly needed. Here, we report a method (LUCK, Laser UV Cross-linKing) to in vivo cross-link proteins by UV-laser irradiation of living cells. Upon irradiation of HeLa cells under controlled conditions, cross-linked products of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were detected, whose yield was found to be a linear function of the total irradiation energy. We demonstrated that stable dimers of GAPDH were formed through intersubunit cross-linking, as also observed when the pure protein was irradiated by UV-laser in vitro. We proposed a defined patch of aromatic residues located at the enzyme subunit interface as the cross-linking sites involved in dimer formation. Hence, by this technique, UV-laser is able to photofix protein surfaces that come in direct contact. Due to the ultra-short time scale of UV-laser-induced cross-linking, this technique could be extended to weld even transient protein interactions in their native context.
Collapse
Affiliation(s)
- Francesco Itri
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Daria M Monti
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy
| | | | - Roberto Vinciguerra
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Felice Gesuele
- Department of Physics, University of Naples Federico II, 80126, Naples, Italy
| | - Angelina Lombardi
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Raffaele Velotta
- Department of Physics, University of Naples Federico II, 80126, Naples, Italy
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR, Naples, Italy
| | - Carlo Altucci
- Department of Physics, University of Naples Federico II, 80126, Naples, Italy.
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR, Naples, Italy.
| | - Leila Birolo
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.
| | - Renata Piccoli
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy.
| |
Collapse
|
46
|
Cohen DT, Zhang C, Pentelute BL, Buchwald SL. An Umpolung Approach for the Chemoselective Arylation of Selenocysteine in Unprotected Peptides. J Am Chem Soc 2015. [PMID: 26225900 PMCID: PMC4613869 DOI: 10.1021/jacs.5b05447] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Herein
we report an umpolung strategy for the bioconjugation of
selenocysteine in unprotected peptides. This mild and operationally
simple approach takes advantage of the electrophilic character of
an oxidized selenocysteine (Se–S bond) to react with a nucleophilic
arylboronic acid to provide the arylated selenocysteine within hours.
This reaction is amenable to a wide range of boronic acids with different
biorelevant functional groups and is unique to selenocysteine. Experimental
evidence indicates that under oxidative conditions the arylated derivatives
are more stable than the corresponding alkylated selenocysteine.
Collapse
Affiliation(s)
- Daniel T Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chi Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stephen L Buchwald
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
47
|
Hennig J, Sattler M. Deciphering the protein-RNA recognition code: Combining large-scale quantitative methods with structural biology. Bioessays 2015; 37:899-908. [DOI: 10.1002/bies.201500033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Janosch Hennig
- Institute of Structural Biology; Helmholtz Zentrum M; ü; nchen; München Germany
- Department Chemie; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy; Technische Universität München; Garching Germany
| | - Michael Sattler
- Institute of Structural Biology; Helmholtz Zentrum M; ü; nchen; München Germany
- Department Chemie; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy; Technische Universität München; Garching Germany
| |
Collapse
|
48
|
Johnson R. Bait and switch. Nat Chem 2014. [DOI: 10.1038/nchem.2077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|