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Baquero F, Beis K, Craik DJ, Li Y, Link AJ, Rebuffat S, Salomón R, Severinov K, Zirah S, Hegemann JD. The pearl jubilee of microcin J25: thirty years of research on an exceptional lasso peptide. Nat Prod Rep 2024; 41:469-511. [PMID: 38164764 DOI: 10.1039/d3np00046j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Covering: 1992 up to 2023Since their discovery, lasso peptides went from peculiarities to be recognized as a major family of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products that were shown to be spread throughout the bacterial kingdom. Microcin J25 was first described in 1992, making it one of the earliest known lasso peptides. No other lasso peptide has since then been studied to such an extent as microcin J25, yet, previous review articles merely skimmed over all the research done on this exceptional lasso peptide. Therefore, to commemorate the 30th anniversary of its first report, we give a comprehensive overview of all literature related to microcin J25. This review article spans the early work towards the discovery of microcin J25, its biosynthetic gene cluster, and the elucidation of its three-dimensional, threaded lasso structure. Furthermore, the current knowledge about the biosynthesis of microcin J25 and lasso peptides in general is summarized and a detailed overview is given on the biological activities associated with microcin J25, including means of self-immunity, uptake into target bacteria, inhibition of the Gram-negative RNA polymerase, and the effects of microcin J25 on mitochondria. The in vitro and in vivo models used to study the potential utility of microcin J25 in a (veterinary) medicine context are discussed and the efforts that went into employing the microcin J25 scaffold in bioengineering contexts are summed up.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Network Center for Research in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, 4072 Brisbane, Queensland, Australia
| | - Yanyan Li
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - A James Link
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Raúl Salomón
- Instituto de Química Biológica "Dr Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany.
- Department of Pharmacy, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
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Digal L, Samson SC, Stevens MA, Ghorai A, Kim H, Mifflin MC, Carney KR, Williamson DL, Um S, Nagy G, Oh DC, Mendoza MC, Roberts AG. Nonthreaded Isomers of Sungsanpin and Ulleungdin Lasso Peptides Inhibit H1299 Cancer Cell Migration. ACS Chem Biol 2024; 19:81-88. [PMID: 38109560 DOI: 10.1021/acschembio.3c00525] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Lasso peptides are a structurally distinct class of biologically active natural products defined by their short sequences with impressively interlocked tertiary structures. Their characteristic peptide [1]rotaxane motif confers marked proteolytic and thermal resiliency, and reports on their diverse biological functions have been credited to their exceptional sequence variability. Because of these unique properties, taken together with improved technologies for their biosynthetic production, lasso peptides are emerging as a designable scaffold for peptide-based therapeutic discovery and development. Although the defined structure of lasso peptides is recognized for its remarkable properties, the role of the motif in imparting bioactivity is less understood. For example, sungsanpin and ulleungdin are natural lasso peptides that similarly exhibit encouraging cell migration inhibitory activities in A549 lung carcinoma epithelial cells, despite sharing only one-third of the sequence homology. We hypothesized that the shape of the lasso motif is beneficial for the preorganization of the conserved residues, which might be partially retained in variants lacking the threaded structure. Herein, we describe solid-phase peptide synthesis strategies to prepare acyclic, head-to-side chain (branched), and head-to-tail (macrocyclic) cyclic variants based on the sungsanpin (Sun) and ulleungdin (Uln) sequences. Proliferation assays and time-lapse cell motility imaging studies were used to evaluate the cell inhibitory properties of natural Sun compared with the synthetic Sun and Uln isomers. These studies demonstrate that the lasso motif is not a required feature to slow cancer cell migration and more generally show that these nonthreaded isomers can retain similar activity to the natural lasso peptide despite the differences in their overall structures.
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Affiliation(s)
- Lori Digal
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Shiela C Samson
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, Utah 84112, United States
| | - Mark A Stevens
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Abhijit Ghorai
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Hyungyu Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Marcus C Mifflin
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Keith R Carney
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, Utah 84112, United States
| | - David L Williamson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Soohyun Um
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Incheon 21983, Republic of Korea
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Michelle C Mendoza
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, Utah 84112, United States
| | - Andrew G Roberts
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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Lee J, Im D, Liu Y, Fang J, Tian X, Kim M, Zhang WB, Seo J. Distinguishing Protein Chemical Topologies Using Supercharging Ion Mobility Spectrometry-Mass Spectrometry. Angew Chem Int Ed Engl 2023; 62:e202314980. [PMID: 37937859 DOI: 10.1002/anie.202314980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/09/2023]
Abstract
A technique combining ion mobility spectrometry-mass spectrometry (IMS-MS) and supercharging electrospray ionization (ESI) has been demonstrated to differentiate protein chemical topology effectively. Incorporating as many charges as possible into proteins via supercharging ESI allows the protein chains to be largely unfolded and stretched, revealing their hidden chemical topology. Different chemical topologies result in differing geometrical sizes of the unfolded proteins due to constraints in torsional rotations in cyclic domains. By introducing new topological indices, such as the chain-length-normalized collision cross-section (CCS) and the maximum charge state (zM ) in the extensively unfolded state, we were able to successfully differentiate various protein chemical topologies, including linear chains, ring-containing topologies (lasso, tadpole, multicyclics, etc.), and mechanically interlocked rings, like catenanes.
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Affiliation(s)
- Jiyeon Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, 37673, Gyeonsangbuk-do (Republic of, Korea
| | - Dahye Im
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, 37673, Gyeonsangbuk-do (Republic of, Korea
| | - Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Xibao Tian
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Minsu Kim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, 37673, Gyeonsangbuk-do (Republic of, Korea
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Jongcheol Seo
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, 37673, Gyeonsangbuk-do (Republic of, Korea
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Xu X, Han L, Zheng Z, Zhao R, Li L, Shao X, Li G. Composite Multidimensional Ion Mobility-Mass Spectrometry for Improved Differentiation of Stereochemical Modifications. Anal Chem 2023; 95:2221-2228. [PMID: 36635260 DOI: 10.1021/acs.analchem.2c03522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Stereochemical modifications (SCMs), mostly present in the form of d-amino acid substitution, have been increasingly identified from a wide range of neuropeptides and disease-associated biomarker proteins. Traditional mass spectrometry-based SCM identification has been effectively enhanced with technological and strategic advancements in ion mobility spectrometry. With the additional separation provided by ion mobility, SCM-induced structural changes can be probed both in theory and in practice, although the structural resolution for low-abundance SCMs still requires further improvement to enable accurate quantification or unambiguous identification of stereoisomers. Herein, we present a multi-component-enabled multidimensional ion mobility-mass spectrometry (3M-IM-MS) analytical workflow, based upon the metal-enhanced chiral amplification strategy we proposed previously (Nat. Commun., 2019, 5038). Notably, the 3M-IM-MS strategy comprises and features the powerful mathematical tools of continuous wavelet transform and Gaussian fitting-enabled peak splitting. Consequently, the resolving capability of ion mobility spectrometry for SCM analysis has been significantly enhanced, providing mobility profiles with baseline separation and more than fivefold improvement in resolving power and overall resolution. This study represents an alternative toward ultrahigh-resolution structural interrogation of mixtures with very small differences, featuring an important and long-lasting topic in chemical measurement.
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Affiliation(s)
- Xia Xu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Li Han
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhen Zheng
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Rui Zhao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xueguang Shao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Gongyu Li
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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5
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Liu L, Wang Z, Zhang Q, Mei Y, Li L, Liu H, Wang Z, Yang L. Ion Mobility Mass Spectrometry for the Separation and Characterization of Small Molecules. Anal Chem 2023; 95:134-151. [PMID: 36625109 DOI: 10.1021/acs.analchem.2c02866] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Longchan Liu
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Ziying Wang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Qian Zhang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Yuqi Mei
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Linnan Li
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Zhengtao Wang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Li Yang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China.,Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
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6
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Hegemann JD. Combined thermal and carboxypeptidase Y stability assays for probing the threaded fold of lasso peptides. Methods Enzymol 2022; 663:177-204. [PMID: 35168788 DOI: 10.1016/bs.mie.2021.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Lasso peptides are natural products belonging to the superfamily of ribosomally synthesized and post-translationally modified peptides (RiPPs). The defining characteristic of lasso peptides is their threaded structure, which is reminiscent of a lariat knot. When working with lasso peptides, it is therefore of major importance to understand and evidence their threaded folds. While the full elucidation of their three-dimensional structures via NMR spectroscopy or crystallization remains the gold standard, these methods are time-consuming, require large quantities of highly pure lasso peptides, and therefore might not always be applicable. Instead, the unique properties of lasso peptides in context of their behavior at elevated temperatures and toward carboxypeptidase Y treatment can be leveraged as a tool to investigate and evidence the threaded lasso fold using only minute amounts of compound that does not need to be purified first. This chapter will provide insights into the thermal stability properties of lasso peptides and their behavior when treated with carboxypeptidase Y in comparison to a branched-cyclic peptide with the same amino acid sequence. Furthermore, it will be described in detail how to set up a combined thermal and carboxypeptidase Y stability assay and how to analyze its outcomes.
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Affiliation(s)
- Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany.
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7
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Le T, Jeanne Dit Fouque K, Santos-Fernandez M, Navo CD, Jiménez-Osés G, Sarksian R, Fernandez-Lima FA, van der Donk WA. Substrate Sequence Controls Regioselectivity of Lanthionine Formation by ProcM. J Am Chem Soc 2021; 143:18733-18743. [PMID: 34724611 DOI: 10.1021/jacs.1c09370] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Lanthipeptides belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs). The (methyl)lanthionine cross-links characteristic to lanthipeptides are essential for their stability and bioactivities. In most bacteria, lanthipeptides are maturated from single precursor peptides encoded in the corresponding biosynthetic gene clusters. However, cyanobacteria engage in combinatorial biosynthesis and encode as many as 80 substrate peptides with highly diverse sequences that are modified by a single lanthionine synthetase into lanthipeptides of different lengths and ring patterns. It is puzzling how a single enzyme could exert control over the cyclization processes of such a wide range of substrates. Here, we used a library of ProcA3.3 precursor peptide variants and show that it is not the enzyme ProcM but rather its substrate sequences that determine the regioselectivity of lanthionine formation. We also demonstrate the utility of trapped ion mobility spectrometry-tandem mass spectrometry (TIMS-MS/MS) as a fast and convenient method to efficiently separate lanthipeptide constitutional isomers, particularly in cases where the isomers cannot be resolved by conventional liquid chromatography. Our data allowed identification of factors that are important for the cyclization outcome, but also showed that there are no easily identifiable predictive rules for all sequences. Our findings provide a platform for future deep learning approaches to allow such prediction of ring patterns of products of combinatorial biosynthesis.
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Affiliation(s)
- Tung Le
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Miguel Santos-Fernandez
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Claudio D Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Raymond Sarksian
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Francisco Alberto Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
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Hegemann JD, Fouque KJD, Santos-Fernandez M, Fernandez-Lima F. A Bifunctional Leader Peptidase/ABC Transporter Protein Is Involved in the Maturation of the Lasso Peptide Cochonodin I from Streptococcus suis. J Nat Prod 2021; 84:2683-2691. [PMID: 34597519 PMCID: PMC9390802 DOI: 10.1021/acs.jnatprod.1c00514] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Lasso peptides are members of the natural product superfamily of ribosomally synthesized and post-translationally modified peptides (RiPPs). Here, we describe the first lasso peptide originating from a biosynthetic gene cluster belonging to a unique lasso peptide subclade defined by the presence of a bifunctional protein harboring both a leader peptidase (B2) and an ABC transporter (D) domain. Bioinformatic analysis revealed that these clusters also encode homologues of the NisR/NisK regulatory system and the NisF/NisE/NisG immunity factors, which are usually associated with the clusters of antimicrobial class I lanthipeptides, such as nisin, another distinct RiPP subfamily. The cluster enabling the heterologous production of the lasso peptide cochonodin I in E. coli originated from Streptococcus suis LSS65, and the threaded structure of cochonodin I was evidenced through extensive MS/MS analysis and stability assays. It was shown that the ABC transporter domain from SsuB2/D is not essential for lasso peptide maturation. By extensive genome mining dedicated exclusively to other lasso peptide biosynthetic gene clusters featuring bifunctional B2/D proteins, it was furthermore revealed that many bacteria associated with human or animal microbiota hold the biosynthetic potential to produce cochonodin-like lasso peptides, implying that these natural products might play roles in human and animal health.
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Affiliation(s)
- Julian D. Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
- Corresponding Author: (J. D. Hegemann):
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Miguel Santos-Fernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
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9
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Deslignière E, Botzanowski T, Diemer H, Cooper-Shepherd DA, Wagner-Rousset E, Colas O, Béchade G, Giles K, Hernandez-Alba O, Beck A, Cianférani S. High-Resolution IMS-MS to Assign Additional Disulfide Bridge Pairing in Complementarity-Determining Regions of an IgG4 Monoclonal Antibody. J Am Soc Mass Spectrom 2021; 32:2505-2512. [PMID: 34437803 DOI: 10.1021/jasms.1c00151] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Monoclonal antibodies (mAbs) have taken on an increasing importance for the treatment of various diseases, including cancers and immunological disorders. Disulfide bonds play a pivotal role in therapeutic antibody structure and activity relationships. Disulfide connectivity and cysteine-related variants are considered as critical quality attributes that must be monitored during mAb manufacturing and storage, as non-native disulfide bridges and aggregates might be responsible for loss of biological function and immunogenicity. The presence of cysteine residues in the complementarity-determining regions (CDRs) is rare in human antibodies but may be critical for the antigen-binding or deleterious for therapeutic antibody development. Consequently, in-depth characterization of their disulfide network is a prerequisite for mAb developability assessment. Mass spectrometry (MS) techniques represent powerful tools for accurate identification of disulfide connectivity. We report here on the MS-based characterization of an IgG4 comprising two additional cysteine residues in the CDR of its light chain. Classical bottom-up approaches after trypsin digestion first allowed identification of a dipeptide containing two disulfide bridges. To further investigate the conformational heterogeneity of the disulfide-bridged dipeptide, we performed ion mobility spectrometry-mass spectrometry (IMS-MS) experiments. Our results highlight benefits of high resolution IMS-MS to tackle the conformational landscape of disulfide peptides generated after trypsin digestion of a humanized IgG4 mAb under development. By comparing arrival time distributions of the mAb-collected and synthetic peptides, cyclic IMS afforded unambiguous assessment of disulfide bonds. In addition to classical peptide mapping, qualitative high-resolution IMS-MS can be of great interest to identify disulfide bonds within therapeutic mAbs.
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Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | | | - Elsa Wagner-Rousset
- IRPF - Centre d'Immunologie Pierre-Fabre (CIPF), 74160 Saint-Julien-en-Genevois, France
| | - Olivier Colas
- IRPF - Centre d'Immunologie Pierre-Fabre (CIPF), 74160 Saint-Julien-en-Genevois, France
| | - Guillaume Béchade
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, Cheshire SK9 4AX, U.K
| | - Kevin Giles
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, Cheshire SK9 4AX, U.K
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Alain Beck
- IRPF - Centre d'Immunologie Pierre-Fabre (CIPF), 74160 Saint-Julien-en-Genevois, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
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10
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Jeanne Dit Fouque K, Hegemann JD, Santos-Fernandez M, Le TT, Gomez-Hernandez M, van der Donk WA, Fernandez-Lima F. Exploring structural signatures of the lanthipeptide prochlorosin 2.8 using tandem mass spectrometry and trapped ion mobility-mass spectrometry. Anal Bioanal Chem 2021; 413:4815-24. [PMID: 34105020 DOI: 10.1007/s00216-021-03437-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 10/21/2022]
Abstract
Lanthipeptides are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by intramolecular thioether cross-links formed between a dehydrated serine/threonine (dSer/dThr) and a cysteine residue. Prochlorosin 2.8 (Pcn2.8) is a class II lanthipeptide that exhibits a non-overlapping thioether ring pattern, for which no biological activity has been reported yet. The variant Pcn2.8[16RGD] has been shown to bind tightly to the αvβ3 integrin receptor. In the present work, tandem mass spectrometry, using collision-induced dissociation (CID) and electron capture dissociation (ECD), and trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) were used to investigate structural signatures for the non-overlapping thioether ring pattern of Pcn2.8. CID experiments on Pcn2.8 yielded bi and yj fragments between the thioether cross-links, evidencing the presence of a non-overlapping thioether ring pattern. ECD experiments of Pcn2.8 showed a significant increase of hydrogen migration events near the residues involved in the thioether rings with a more pronounced effect at the dehydrated residues as compared to the cysteine residues. The high-resolution mobility analysis, aided by site-directed mutagenesis ([P8A], [P11A], [P12A], [P8A/P11A], [P8A/P12A], [P11A/P12A], and [P8A/P11A/P12A] variants), demonstrated that Pcn2.8 adopts cis/trans-conformations at Pro8, Pro11, and Pro12 residues. These observations were complementary to recent NMR findings, for which only the Pro8 residue was evidenced to adopt cis/trans-orientations. This study highlights the analytical power of the TIMS-MS/MS workflow for the structural characterization of lanthipeptides and could be a useful tool in our understanding of the biologically important structural elements that drive the thioether cyclization process.
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11
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Weerasinghe NW, Habibi Y, Uggowitzer KA, Thibodeaux CJ. Exploring the Conformational Landscape of a Lanthipeptide Synthetase Using Native Mass Spectrometry. Biochemistry 2021; 60:1506-1519. [PMID: 33887902 DOI: 10.1021/acs.biochem.1c00085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. These genetically encoded peptides are biosynthesized by multifunctional enzymes (lanthipeptide synthetases) that possess relaxed substrate specificity and catalyze iterative rounds of post-translational modification. Recent evidence has suggested that some lanthipeptide synthetases are structurally dynamic enzymes that are allosterically activated by precursor peptide binding and that conformational sampling of the enzyme-peptide complex may play an important role in defining the efficiency and sequence of biosynthetic events. These "biophysical" processes, while critical for defining the activity and function of the synthetase, remain very challenging to study with existing methodologies. Herein, we show that native mass spectrometry coupled to ion mobility (native IM-MS) provides a powerful and sensitive means for investigating the conformational landscapes and intermolecular interactions of lanthipeptide synthetases. Namely, we demonstrate that the class II lanthipeptide synthetase (HalM2) and its noncovalent complex with the cognate HalA2 precursor peptide can be delivered into the gas phase in a manner that preserves native structures and intermolecular enzyme-peptide contacts. Moreover, gas phase ion mobility studies of the natively folded ions demonstrate that peptide binding and mutations to dynamic structural elements of HalM2 alter the conformational landscape of the enzyme. Cumulatively, these data support previous claims that lanthipeptide synthetases are structurally dynamic enzymes that undergo functionally relevant conformational changes in response to precursor peptide binding. This work establishes native IM-MS as a versatile approach for characterizing intermolecular interactions and for unraveling the relationships between protein structure and biochemical function in RiPP biosynthetic systems.
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Affiliation(s)
- Nuwani W Weerasinghe
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Yeganeh Habibi
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Kevin A Uggowitzer
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Christopher J Thibodeaux
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
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12
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Dit Fouque KJ, Scutelnic V, Hegemann JD, Rebuffat S, Maître P, Rizzo TR, Fernandez-Lima F. Structural Insights from Tandem Mass Spectrometry, Ion Mobility-Mass Spectrometry, and Infrared/Ultraviolet Spectroscopy on Sphingonodin I: Lasso vs Branched-Cyclic Topoisomers. J Am Soc Mass Spectrom 2021; 32:1096-1104. [PMID: 33765377 DOI: 10.1021/jasms.1c00041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lasso peptides form a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by a mechanically interlocked topology, where the C-terminal tail of the peptide is threaded and trapped within an N-terminal macrolactam ring. Sphingonodin I is a lasso peptide that has not yet been structurally characterized using the traditional structural biology tools (e.g., NMR and X-ray crystallography), and its biological function has not yet been elucidated. In the present work, we describe structural signatures characteristic of the class II lasso peptide sphingonodin I and its branched-cyclic analogue using a combination of gas-phase ion tools (e.g., tandem mass spectrometry, MS/MS, trapped ion mobility spectrometry, TIMS, and infrared, IR, and ultraviolet, UV, spectroscopies). Tandem MS/MS CID experiments on sphingonodin I yielded mechanically interlocked species with associated bi and yj fragments demonstrating the presence of a lasso topology, while tandem MS/MS ECD experiments on sphingonodin I showed a significant increase in hydrogen migration in the loop region when compared to the branched-cyclic analogue. The high-mobility resolving power of TIMS permitted the separation of both topoisomers, where sphingonodin I adopted a more compact structure than its branched-cyclic analogue. Cryogenic and room-temperature IR spectroscopy experiments evidenced a different hydrogen bond network between the two topologies, while cryogenic UV spectroscopy experiments clearly demonstrated a distinct phenylalanine environment for the lasso peptide.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, AHC4-233, Miami, Florida 33199, United States
| | - Valeriu Scutelnic
- Laboratory of Molecular Physical Chemistry, Ecole Polytechnique Fedérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Julian D Hegemann
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms, National Museum of Natural History, CNRS, 57 rue Cuvier, CP-54, 75005 Paris, France
| | - Philippe Maître
- Laboratoire de Chimie Physique, Université Paris Sud, UMR 8000 CNRS, Faculté des Sciences, Bât. 349, 91405 Orsay Cedex France
| | - Thomas R Rizzo
- Laboratory of Molecular Physical Chemistry, Ecole Polytechnique Fedérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, AHC4-233, Miami, Florida 33199, United States
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13
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Rivera ES, Djambazova KV, Neumann EK, Caprioli RM, Spraggins JM. Integrating ion mobility and imaging mass spectrometry for comprehensive analysis of biological tissues: A brief review and perspective. J Mass Spectrom 2020; 55:e4614. [PMID: 32955134 PMCID: PMC8211109 DOI: 10.1002/jms.4614] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 05/02/2023]
Abstract
Imaging mass spectrometry (IMS) technologies are capable of mapping a wide array of biomolecules in diverse cellular and tissue environments. IMS has emerged as an essential tool for providing spatially targeted molecular information due to its high sensitivity, wide molecular coverage, and chemical specificity. One of the major challenges for mapping the complex cellular milieu is the presence of many isomers and isobars in these samples. This challenge is traditionally addressed using orthogonal liquid chromatography (LC)-based analysis, though, common approaches such as chromatography and electrophoresis are not able to be performed at timescales that are compatible with most imaging applications. Ion mobility offers rapid, gas-phase separations that are readily integrated with IMS workflows in order to provide additional data dimensionality that can improve signal-to-noise, dynamic range, and specificity. Here, we highlight recent examples of ion mobility coupled to IMS and highlight their importance to the field.
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Key Words
- IMS
- desorption electrospray ionization, DESI
- drift tube ion mobility spectrometry, DTIMS
- high-field asymmetric waveform ion mobility, FAIMS
- imaging mass spectrometry
- infrared matrix-assisted laser desorption electrospray ionization, IR-MALDESI
- ion mobility
- laser ablation electrospray ionization, LAESI
- lipids
- liquid extraction surface analysis, LESA
- liquid microjunction, (LMJ)
- matrix-assisted laser desorption electrospray ionization, MALDI
- metabolites
- proteins
- tissue analysis
- trapped ion mobility spectrometry, TIMS
- travelling wave ion mobility spectrometry, TWIMS
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Affiliation(s)
- Emilio S. Rivera
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Katerina V. Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
| | - Elizabeth K. Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Jeffrey M. Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
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Liu Y, Wu W, Hong S, Fang J, Zhang F, Liu G, Seo J, Zhang W. Lasso Proteins: Modular Design, Cellular Synthesis, and Topological Transformation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yajie Liu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Wen‐Hao Wu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Sumin Hong
- Department of Chemistry Pohang University of Science and Technology (POSTECH) Pohang 37673 Republic of Korea
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Fan Zhang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Geng‐Xin Liu
- Center for Advanced Low-dimension Materials State Key Laboratory for Modification of Chemical Fibers and Polymer Materials College of Material Science and Engineering Donghua University Shanghai 201620 China
| | - Jongcheol Seo
- Department of Chemistry Pohang University of Science and Technology (POSTECH) Pohang 37673 Republic of Korea
| | - Wen‐Bin Zhang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
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15
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Jarmusch SA, Feldmann I, Blank-landeshammer B, Cortés-albayay C, Castro JF, Andrews B, Asenjo JA, Sickmann A, Ebel R, Jaspars M. Cutting the Gordian knot: early and complete amino acid sequence confirmation of class II lasso peptides by HCD fragmentation. J Antibiot (Tokyo) 2020; 73:772-9. [DOI: 10.1038/s41429-020-00369-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023]
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16
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Liu Y, Wu WH, Hong S, Fang J, Zhang F, Liu GX, Seo J, Zhang WB. Lasso Proteins: Modular Design, Cellular Synthesis, and Topological Transformation. Angew Chem Int Ed Engl 2020; 59:19153-19161. [PMID: 32602613 DOI: 10.1002/anie.202006727] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/30/2020] [Indexed: 02/06/2023]
Abstract
Entangled proteins have attracted significant research interest. Herein, we report the first rationally designed lasso proteins, or protein [1]rotaxanes, by using a p53dim-entwined dimer for intramolecular entanglement and a SpyTag-SpyCatcher reaction for side-chain ring closure. The lasso structures were confirmed by proteolytic digestion, mutation, NMR spectrometry, and controlled ligation. Their dynamic properties were probed by experiments such as end-capping, proteolytic digestion, and heating/cooling. As a versatile topological intermediate, a lasso protein could be converted to a rotaxane, a heterocatenane, and a "slide-ring" network. Being entirely genetically encoded, this robust and modular lasso-protein motif is a valuable addition to the topological protein repertoire and a promising candidate for protein-based biomaterials.
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Affiliation(s)
- Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Sumin Hong
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Geng-Xin Liu
- Center for Advanced Low-dimension Materials, State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Jongcheol Seo
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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17
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Schmitz T, Pengelley S, Belau E, Suckau D, Imhof D. LC-Trapped Ion Mobility Spectrometry-TOF MS Differentiation of 2- and 3-Disulfide-Bonded Isomers of the μ-Conotoxin PIIIA. Anal Chem 2020; 92:10920-10924. [PMID: 32806900 DOI: 10.1021/acs.analchem.0c02151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Disulfide bonds within cysteine-rich peptides are important for their stability and biological function. In this respect, the correct disulfide connectivity plays a decisive role. The differentiation of individual disulfide-bonded isomers by traditional high-performance liquid chromatography (HPLC) and mass spectrometry (MS) is limited due to the similarity in physicochemical properties of the isomers sharing the same amino acid sequence. By using trapped ion mobility spectrometry-mass spectrometry (TIMS-MS), several 2- and 3-disulfide-bonded isomers of the μ-conotoxin PIIIA were investigated for their distinguishability by collision cross section (CCS) values and their characteristic mobilogram traces. The isomers could be differentiated by TIMS-MS and also identified in mixing experiments. Thus, TIMS-MS provides a highly valuable and enriching addition to standard HPLC and MS analysis of conformational isomers of disulfide-rich peptides and proteins.
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Affiliation(s)
- Thomas Schmitz
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Stuart Pengelley
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Eckhard Belau
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Detlev Suckau
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
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18
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Li G, Delafield DG, Li L. Improved structural elucidation of peptide isomers and their receptors using advanced ion mobility-mass spectrometry. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.05.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Abstract
Native ion mobility-mass spectrometry (IM-MS) is an emerging biophysical approach to probe the intricate details of protein structure and function. The instrument design enables measurements of accurate first-principle determinations of rotationally-averaged ion-neutral collision cross sections coupled with high-mass, high-resolution mass measurement capabilities of Orbitrap MS. The inherent duty-cycle mismatch between drift tube IM and Orbitrap MS is alleviated by operating the drift tube in a frequency modulated mode while continuously acquiring mass spectra with the Orbitrap MS. Fourier transform of the resulting time-domain signal, i.e., ion abundances as a function of the modulation frequency, yields a frequency domain spectrum that is then converted (s-1 to s) to IM drift time. This multiplexed approach allows for a duty-cycle of 25% compared to <1% for traditional "pulse-and-wait" IM-ToF-MS. Improvements in mobility and mass resolution of the IM-Orbitrap allows for accurate analysis of intact protein complexes and the possibility of capturing protein dynamics.
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Affiliation(s)
- Michael L. Poltash
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843
| | - Jacob W. McCabe
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843
| | - David H. Russell
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843
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20
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Affiliation(s)
- Julian D. Hegemann
- Technische Universität BerlinInstitute of Chemistry Strasse des 17. Juni 124/TC2 10623 Berlin Germany
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21
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22
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Jeanne Dit Fouque K, Fernandez-Lima F. Recent advances in biological separations using trapped ion mobility spectrometry – mass spectrometry. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.04.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Jeanne Dit Fouque K, Hegemann JD, Zirah S, Rebuffat S, Lescop E, Fernandez-Lima F. Evidence of Cis/Trans-Isomerization at Pro7/Pro16 in the Lasso Peptide Microcin J25. J Am Soc Mass Spectrom 2019; 30:1038-1045. [PMID: 30834511 DOI: 10.1007/s13361-019-02134-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
Microcin J25 is a ribosomal synthesized and post-translationally modified peptide (RiPP) characterized by a mechanically interlocked topology called the lasso fold. This structure provides microcin J25 a potent antimicrobial activity resulting from internalization via the siderophore receptor FhuA and further inhibition of the RNA polymerase. In the present work, nuclear magnetic resonance (NMR) and trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) were used to investigate the lasso structure of microcin J25. NMR experiments showed that the lasso peptide microcin J25 can adopt conformational states where Pro16 can be found in the cis- and trans-orientations. The high-resolution mobility analysis, aided by site-directed mutagenesis ([P7A], [P16A], and [P7A/P16A] variants), demonstrated that microcin J25 can adopt cis/cis-, cis/trans-, trans/cis-, and trans/trans-conformations at the Pro7 and Pro16 peptide bonds. It was also shown that interconversion between the conformers can occur as a function of the starting solvent conditions and ion heating (collision-induced activation, CIA) despite the lasso topology. Complementary to NMR findings, the cis-conformations at Pro7 were assigned using TIMS-MS. This study highlights the analytical power of TIMS-MS and site-directed mutagenesis for the study of biological systems with large micro-heterogeneity as a way to further increase our understanding of the receptor-binding dynamics and biological activity.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., AHC4-233, Miami, FL, 33199, USA
| | - Julian D Hegemann
- M Department of Chemistry, University of Illinois, Urbana-Champaign, IL, 61801, USA
| | - Séverine Zirah
- Laboratory Molecules of Communication and Adaptation of Microorganisms, National Museum of Natural History, CNRS UMR 7245, 75005, Paris, France
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms, National Museum of Natural History, CNRS UMR 7245, 75005, Paris, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198, Gif sur Yvette Cedex, France
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., AHC4-233, Miami, FL, 33199, USA.
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24
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Boutin JA, Tartar AL, van Dorsselaer A, Vaudry H. General lack of structural characterization of chemically synthesized long peptides. Protein Sci 2019; 28:857-867. [PMID: 30851143 PMCID: PMC6459998 DOI: 10.1002/pro.3601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 01/01/2023]
Abstract
Many peptide chemistry scientists have been reporting extremely interesting work on the basis of chemical peptides for which the only characterization was their purity, mass, and biological activity. It seems slightly overenthusiastic, as many of these structures should be thoroughly characterized first to demonstrate the uniqueness of the structure, as opposed to the uniqueness of the sequence. Among the peptides of identical sequences in the final chemical preparation, what amount of well-folded peptide supports the measured activity? The activity of a peptide preparation cannot prove the purity of the desired peptide. Therefore, greater care should be taken in characterizing peptides, particularly those coming from chemical synthesis. At a time when the pharmaceutical industry is changing its paradigm by moving substantially from small molecules to biologics to better serve patients' needs, it is important to understand the limitations of the descriptions of these products and to start to apply the same "good laboratory practices" to our peptide research. Here, we attempt to delineate how synthetic peptides are described and characterized and what will be needed to describe them in regards to how they are well-folded and homogeneous in their tertiary structure. Older studies were done when the tools were not yet discovered, but more recent publications are still lacking proper descriptions of these peptides. Modern tools of analysis are capable of segregating folded and unfolded peptides, even if the preparation is biologically active.
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Affiliation(s)
- Jean A. Boutin
- Institut de Recherches Internationales Servier50 rue Carnot, 92284, Suresnes‐CedexFrance
| | - André L. Tartar
- Faculté de Pharmacie 3rue du Professeur Laguesse, BP83 ‐ 59006, Lille‐CedexFrance
| | - Alain van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio‐Organique, Département des Sciences AnalytiquesInstitut Pluridisciplinaire Hubert CurienUMR 7178 (CNRS‐UdS), ECPM, 25 rue Becquerel, F67087, Strasbourg‐Cedex 2France
| | - Hubert Vaudry
- Plate‐Forme de Recherche en Imagerie Cellulaire de Normandie (PRIMACEN)Institut de Recherche et d'Innovation Biomédicales (IRIB), Université de Rouen76821, Mont‐Saint‐Aignan CedexFrance
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25
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Zhu S, Su Y, Shams S, Feng Y, Tong Y, Zheng G. Lassomycin and lariatin lasso peptides as suitable antibiotics for combating mycobacterial infections: current state of biosynthesis and perspectives for production. Appl Microbiol Biotechnol 2019; 103:3931-3940. [PMID: 30915503 DOI: 10.1007/s00253-019-09771-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 11/30/2022]
Abstract
Lasso peptides are ribosomally synthesized and post-translationally modified natural products with a characteristic slipknot-like structure, which confers these peptides remarkable stability and diverse pharmacologically relevant bioactivities. Among all the reported lasso peptides, lassomycin and lariatins are unique lasso peptides that exhibit noticeable anti-tuberculosis (TB) activity. Due to the unique threaded structure and the unusual bactericidal mechanism toward Mycobacterium tuberculosis, these peptides have drawn considerable interest, not only in the field of total synthesis but also in several other fields including biosynthesis, bioengineering, and structure-activity studies. During the past few years, significant progress has been made in understanding the biosynthetic mechanism of these intriguing compounds, which has provided a solid foundation for future work. This review highlights recent achievements in the discovery, structure elucidation, biological activity, and the unique anti-TB mechanism of lasso peptides. Moreover, the discovery of their biosynthetic pathway has laid the foundation for combinatorial biosynthesis of their analogs, which provides new perspectives for the production of novel anti-TB lasso peptides.
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Affiliation(s)
- Shaozhou Zhu
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
| | - Yu Su
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Saira Shams
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yue Feng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yigang Tong
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Guojun Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
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Jeanne Dit Fouque K, Garabedian A, Leng F, Tse-Dinh YC, Fernandez-Lima F. Microheterogeneity of Topoisomerase IA/IB and Their DNA-Bound States. ACS Omega 2019; 4:3619-3626. [PMID: 30842985 PMCID: PMC6396120 DOI: 10.1021/acsomega.8b02887] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 01/11/2019] [Indexed: 05/14/2023]
Abstract
Topoisomerases are important complex enzymes that modulate DNA topology to maintain chromosome superstructure and integrity. These enzymes are involved in many cellular processes that resolve specific DNA superstructures and intermediates. The low abundance combined with the biological heterogeneity of relevant intermediates of topoisomerases makes their structural information not readily accessible using traditional structural biology tools (e.g., NMR and X-ray crystallography). In the present work, a second-generation trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) was used to study Escherichia coli topoisomerase IA (EcTopIA) and variola virus topoisomerase IB (vTopIB) as well as their complexes with a single-stranded DNA and a stem-loop DNA under native conditions. The higher trapping efficiency and extended mass range of the new, convex TIMS geometry allowed for the separation and identification of multiple conformational states for the two topoisomerases and their DNA complexes. Inspection of the conformational space of EcTopIA and vTopIB in complex with DNA showed that upon DNA binding, the number of conformational states is significantly reduced, suggesting that the DNA binding selects for a narrow range of conformers restricted by the interaction with the DNA substrate. The large microheterogeneity observed for the two DNA binding proteins suggests that they can have multiple biological functions. This work highlights the potential of TIMS-MS for the structural investigations of intrinsically disordered proteins (e.g., DNA binding proteins) as a way to gain a better understanding of the mechanisms involved in DNA substrate recognition, binding, and assembly of the catalytically active enzyme-DNA complex.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Alyssa Garabedian
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Fenfei Leng
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Yuk-Ching Tse-Dinh
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
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Jeanne Dit Fouque K, Bisram V, Hegemann JD, Zirah S, Rebuffat S, Fernandez-lima F. Structural signatures of the class III lasso peptide BI-32169 and the branched-cyclic topoisomers using trapped ion mobility spectrometry–mass spectrometry and tandem mass spectrometry. Anal Bioanal Chem 2019; 411:6287-96. [DOI: 10.1007/s00216-019-01613-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 12/14/2018] [Accepted: 01/15/2019] [Indexed: 10/27/2022]
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Martin-Gómez H, Linne U, Albericio F, Tulla-Puche J, Hegemann JD. Investigation of the Biosynthesis of the Lasso Peptide Chaxapeptin Using an E. coli-Based Production System. J Nat Prod 2018; 81:2050-2056. [PMID: 30178995 DOI: 10.1021/acs.jnatprod.8b00392] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lasso peptides are natural products belonging to the family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) and are defined by their unique topology. Even though lasso peptide biosynthetic gene clusters are found in many different kinds of bacteria, most of the hitherto studied lasso peptides were of proteobacterial or actinobacterial origin. Despite this, no E. coli-based production system has been reported for actinobacterial lasso peptides, while there are numerous examples of this for proteobacterial lasso peptides. Here, a heterologous production system of the lasso peptide chaxapeptin was established in E. coli. Chaxapeptin, originally isolated from Streptomyces leeuwenhoekii strain C58, is closely related to the lasso peptide sungsanpin (produced by a marine Streptomyces sp.) and shares its inhibitory activity against cell invasion by the human lung cancer cell line A549. Our production system not only allowed isolation of the mature lasso peptide outside of the native producer with a yield of 0.1 mg/L (compared to 0.7 mg/L from S. leeuwenhoekii) but also was used for a mutational study to identify residues in the precursor peptide that are important for biosynthesis. In addition to these experiments, the stability of chaxapeptin against thermal denaturation and proteases was assessed.
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Affiliation(s)
- Helena Martin-Gómez
- Institute for Research in Biomedicine , Baldiri Reixac 10 , 08028 Barcelona , Spain
- Department of Chemistry , Philipps-University Marburg , Hans-Meerwein-Strasse 4 , 35032 Marburg , Germany
| | - Uwe Linne
- Department of Chemistry , Philipps-University Marburg , Hans-Meerwein-Strasse 4 , 35032 Marburg , Germany
| | - Fernando Albericio
- Department of Inorganic and Organic Chemistry-Organic Chemistry Section , University of Barcelona , Martí i Franquès 1-11 , 08028 Barcelona , Spain
- CIBER-BBN, Networking Centre on Bioengineering , Biomaterials and Nanomedicine , Baldiri Reixac 10 , 08028 Barcelona , Spain
- School of Chemistry and Physics , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Judit Tulla-Puche
- Department of Inorganic and Organic Chemistry-Organic Chemistry Section , University of Barcelona , Martí i Franquès 1-11 , 08028 Barcelona , Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB) , 08028 Barcelona , Spain
| | - Julian D Hegemann
- Department of Chemistry , Philipps-University Marburg , Hans-Meerwein-Strasse 4 , 35032 Marburg , Germany
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 S. Mathews Avenue , Urbana , Illinois 61801 , United States
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Jeanne Dit Fouque K, Moreno J, Hegemann JD, Zirah S, Rebuffat S, Fernandez-Lima F. Metal ions induced secondary structure rearrangements: mechanically interlocked lassovs.unthreaded branched-cyclic topoisomers. Analyst 2018; 143:2323-2333. [DOI: 10.1039/c8an00138c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metal ions can play a significant role in a variety of important functions in protein systems including cofactor for catalysis, protein folding, assembly, structural stability and conformational change.
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Affiliation(s)
| | - Javier Moreno
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | | | - Séverine Zirah
- Laboratory Molecules of Communication and Adaptation of Microorganisms
- National Museum of Natural History
- Sorbonne Univ
- 75005 Paris
- France
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms
- National Museum of Natural History
- Sorbonne Univ
- 75005 Paris
- France
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