1
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Lin Z, Agarwal V, Cong Y, Pomponi SA, Schmidt EW. Short macrocyclic peptides in sponge genomes. Proc Natl Acad Sci U S A 2024; 121:e2314383121. [PMID: 38442178 PMCID: PMC10945851 DOI: 10.1073/pnas.2314383121] [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: 08/22/2023] [Accepted: 01/19/2024] [Indexed: 03/07/2024] Open
Abstract
Sponges (Porifera) contain many peptide-specialized metabolites with potent biological activities and significant roles in shaping marine ecology. It is well established that symbiotic bacteria produce bioactive "sponge" peptides, both on the ribosome (RiPPs) and nonribosomally. Here, we demonstrate that sponges themselves also produce many bioactive macrocyclic peptides, such as phakellistatins and related proline-rich macrocyclic peptides (PRMPs). Using the Stylissa carteri sponge transcriptome, methods were developed to find sequences encoding 46 distinct RiPP-type core peptides, of which ten encoded previously identified PRMP sequences. With this basis set, the genome and transcriptome of the sponge Axinella corrugata was interrogated to find 35 PRMP precursor peptides encoding 31 unique core peptide sequences. At least 11 of these produced cyclic peptides that were present in the sponge and could be characterized by mass spectrometry, including stylissamides A-D and seven previously undescribed compounds. Precursor peptides were encoded in the A. corrugata genome, confirming their animal origin. The peptides contained signal peptide sequences and highly repetitive recognition sequence-core peptide elements with up to 25 PRMP copies in a single precursor. In comparison to sponges without PRMPs, PRMP sponges are incredibly enriched in potentially secreted polypeptides, with >23,000 individual signal peptide encoding genes found in a single transcriptome. The similarities between PRMP biosynthetic genes and neuropeptides in terms of their biosynthetic logic suggest a fundamental biology linked to circular peptides, possibly indicating a widespread and underappreciated diversity of signaling peptide post-translational modifications across the animal kingdom.
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Affiliation(s)
- Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA30332
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332
| | - Ying Cong
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL34946
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
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2
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Lee Y, Kim KM, Nguyen DL, Jannah F, Seong HJ, Kim JM, Kim YP. Cyclized proteins with tags as permeable and stable cargos for delivery into cells and liposomes. Int J Biol Macromol 2023; 252:126520. [PMID: 37625744 DOI: 10.1016/j.ijbiomac.2023.126520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023]
Abstract
Despite the therapeutic potential of recombinant proteins, their cell permeabilities and stabilities remain significant challenges. Here we demonstrate that cyclized recombinant proteins can be used as universal cargos for permeable and stable delivery into cells and polydiacetylene liposomes. Utilizing a split intein-mediated process, cyclized model fluorescent proteins containing short tetraarginine (R4) and hexahistidine (H6) tags were generated without compromising their native protein functions. Strikingly, as compared to linear R4/H6-tagged proteins, the cyclized counterparts have substantially increased permeabilities in both cancer cells and synthetic liposomes, as well as higher resistances to enzymatic degradation in cancer cells. These properties are likely a consequence of structural constraints imposed on the proteins in the presence of short functional peptides. Additionally, photodynamic therapy by cyclized photoprotein-loaded liposomes in cancer cells was significantly improved in comparison to that by their non-cyclized counterparts. These findings suggest that our strategy will be universally applicable to intercellular delivery of proteins and therapeutics.
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Affiliation(s)
- Yeonju Lee
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Kyung-Min Kim
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Duc Long Nguyen
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Fadilatul Jannah
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Hyun-Jung Seong
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Jong-Man Kim
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Republic of Korea; Institute of Nano Science and Technology, Hanyang University, Seoul 04763, Republic of Korea.
| | - Young-Pil Kim
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea; Institute of Nano Science and Technology, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea; Department of HY-KIST Bio-Convergence, Hanyang University, Seoul 04763, Republic of Korea; Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Republic of Korea.
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3
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Randall JR, Wang X, Groover KE, O'Donnell AC, Davies BW. Using display technologies to identify macrocyclic peptide antibiotics. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119473. [PMID: 37011732 PMCID: PMC10198949 DOI: 10.1016/j.bbamcr.2023.119473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 02/09/2023] [Accepted: 02/19/2023] [Indexed: 04/03/2023]
Abstract
Antibiotic resistant bacterial infections are now a leading cause of global mortality. While drug resistance continues to spread, the clinical antibiotic pipeline has become bare. This discord has focused attention on developing new strategies for antimicrobial discovery. Natural macrocyclic peptide-based products have provided novel antibiotics and antibiotic scaffolds targeting several essential bacterial cell envelope processes, but discovery of such natural products remains a slow and inefficient process. Synthetic strategies employing peptide display technologies can quickly screen large libraries of macrocyclic sequences for specific target binding and general antibacterial potential providing alternative approaches for new antibiotic discovery. Here we review cell envelope processes that can be targeted with macrocyclic peptide therapeutics, outline important macrocyclic peptide display technologies, and discuss future strategies for both library design and screening.
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Affiliation(s)
- Justin R Randall
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA.
| | - Xun Wang
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA
| | - Kyra E Groover
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA
| | - Angela C O'Donnell
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA
| | - Bryan W Davies
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA.
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4
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Ciulla MG, Gelain F. Structure-activity relationships of antibacterial peptides. Microb Biotechnol 2023; 16:757-777. [PMID: 36705032 PMCID: PMC10034643 DOI: 10.1111/1751-7915.14213] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/08/2022] [Accepted: 01/01/2023] [Indexed: 01/28/2023] Open
Abstract
Antimicrobial peptides play a crucial role in innate immunity, whose components are mainly peptide-based molecules with antibacterial properties. Indeed, the exploration of the immune system over the past 40 years has revealed a number of natural peptides playing a pivotal role in the defence mechanisms of vertebrates and invertebrates, including amphibians, insects, and mammalians. This review provides a discussion regarding the antibacterial mechanisms of peptide-based agents and their structure-activity relationships (SARs) with the aim of describing a topic that is not yet fully explored. Some growing evidence suggests that innate immunity should be strongly considered for the development of novel antibiotic peptide-based libraries. Also, due to the constantly rising concern of antibiotic resistance, the development of new antibiotic drugs is becoming a priority of global importance. Hence, the study and the understanding of defence phenomena occurring in the immune system may inspire the development of novel antibiotic compound libraries and set the stage to overcome drug-resistant pathogens. Here, we provide an overview of the importance of peptide-based antibacterial sources, focusing on accurately selected molecular structures, their SARs including recently introduced modifications, their latest biotechnology applications, and their potential against multi-drug resistant pathogens. Last, we provide cues to describe how antibacterial peptides show a better scope of action selectivity than several anti-infective agents, which are characterized by non-selective activities and non-targeted actions toward pathogens.
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Affiliation(s)
- Maria Gessica Ciulla
- Institute for Stem-Cell Biology, Regenerative Medicine and Innovative Therapies, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Center for Nanomedicine and Tissue Engineering (CNTE), ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Fabrizio Gelain
- Institute for Stem-Cell Biology, Regenerative Medicine and Innovative Therapies, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Center for Nanomedicine and Tissue Engineering (CNTE), ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
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5
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Jia X, Chin YKY, Zhang AH, Crawford T, Zhu Y, Fletcher NL, Zhou Z, Hamilton BR, Stroet M, Thurecht KJ, Mobli M. Self-cyclisation as a general and efficient platform for peptide and protein macrocyclisation. Commun Chem 2023; 6:48. [PMID: 36871076 PMCID: PMC9985607 DOI: 10.1038/s42004-023-00841-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
Macrocyclisation of proteins and peptides results in a remarkable increase in structural stability, making cyclic peptides and proteins of great interest in drug discovery-either directly as drug leads or as in the case of cyclised nanodiscs (cNDs), as tools for studies of trans-membrane receptors and membrane-active peptides. Various biological methods have been developed that are capable of yielding head-to-tail macrocyclised products. Recent advances in enzyme-catalysed macrocyclisation include discovery of new enzymes or design of new engineered enzymes. Here, we describe the engineering of a self-cyclising "autocyclase" protein, capable of performing a controllable unimolecular reaction for generation of cyclic biomolecules in high yield. We characterise the self-cyclisation reaction mechanism, and demonstrate how the unimolecular reaction path provides alternative avenues for addressing existing challenges in enzymatic cyclisation. We use the method to produce several notable cyclic peptides and proteins, demonstrating how autocyclases offer a simple, alternative way to access a vast diversity of macrocyclic biomolecules.
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Affiliation(s)
- Xinying Jia
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Yanni K-Y Chin
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Alan H Zhang
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Theo Crawford
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Yifei Zhu
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Nicholas L Fletcher
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Zihan Zhou
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Brett R Hamilton
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Martin Stroet
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Kristofer J Thurecht
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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6
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Chowdhury A, Bandyopadhyay A. Compelling Cyclic Peptide Scaffolds for Antitubercular Action: An Account (2011-21) of the Natural Source. Curr Protein Pept Sci 2022; 23:823-836. [PMID: 36200246 DOI: 10.2174/1389203723666220930111259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 01/20/2023]
Abstract
Natural cyclic peptide scaffolds are indispensable in medicinal chemistry, chemical biology, and drug discovery platforms due to their chemical diversity, structural integrity, proteolytic stability and biocompatibility. Historically, their isolation and profound understanding of target engagement have been identified as lead pharmacophore discovery. Natural cyclic peptides are the largest class of pharmacologically active scaffold, in which most show activity against drug-resistant Mycobacterium tuberculosis (Mtb). Nevertheless, eight recently discovered cyclic peptide scaffolds exhibit promising antitubercular activity among numerous naturally occurring antitubercular peptides, and they are amenable scaffolds to drug development. We examined their biological origin, scaffolds, isolations, chemical synthesis, and reasons for biological actions against Mtb. Understanding these peptide scaffold details will further allow synthetic and medicinal chemists to develop novel peptide therapeutics against tuberculosis-infected deadly diseases. This review emphasizes these cyclic peptides' in vitro and in vivo activity profiles, including their structural and chemical features.
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Affiliation(s)
- Arnab Chowdhury
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Punjab- 140001, India
| | - Anupam Bandyopadhyay
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Punjab- 140001, India
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7
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Luo J, Liu S, Lu H, Chen Q, Shi Y. A comprehensive review of microorganism-derived cyclic peptides: Bioactive functions and food safety applications. Compr Rev Food Sci Food Saf 2022; 21:5272-5290. [PMID: 36161470 DOI: 10.1111/1541-4337.13038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/09/2022] [Accepted: 08/21/2022] [Indexed: 01/28/2023]
Abstract
Cyclic peptides possess advanced structural characteristics of stability and play a vital role in medical treatment and agriculture. However, the biological functions of microorganism-derived cyclic peptides (MDCPs) and their applications in food industry were relatively absent. MDCPs are derived from extensive fermented food or soil. In this review, the synthesis approaches and structural characteristics are overviewed, while the interrelationship between bioactivities and functions is emphasized. This review summarizes the bioactivities of MDCPs from in vitro to in vivo, including antimicrobial activities, immune regulation, and antiviral cell activation. Their multiple functions as well as applications during food product processing, packaging, and storage are also comprehensively reviewed. Remarkably, some potential risks and cytotoxicity of MDCPs are also critically discussed. Moreover, future applications of MDCPs in the development of novel food additives and bioengineering materials are organized. Based on this review of native MDCPs, it is noteworthy that expected improvements of synthetic cyclic peptides in bioactive properties present potential valuable applications in future food, including artificial meat.
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Affiliation(s)
- Jiaqi Luo
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Siyu Liu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Hongyun Lu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Qihe Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Ying Shi
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
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8
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Elashal HE, Koos JD, Cheung-Lee WL, Choi B, Cao L, Richardson MA, White HL, Link AJ. Biosynthesis and characterization of fuscimiditide, an aspartimidylated graspetide. Nat Chem 2022; 14:1325-1334. [PMID: 35982233 PMCID: PMC10078976 DOI: 10.1038/s41557-022-01022-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/11/2022] [Indexed: 11/09/2022]
Abstract
Microviridins and other ω-ester-linked peptides, collectively known as graspetides, are characterized by side-chain-side-chain linkages installed by ATP-grasp enzymes. Here we report the discovery of a family of graspetides, the gene clusters of which also encode an O-methyltransferase with homology to the protein repair catalyst protein L-isoaspartyl methyltransferase. Using heterologous expression, we produced fuscimiditide, a ribosomally synthesized and post-translationally modified peptide (RiPP). NMR analysis of fuscimiditide revealed that the peptide contains two ester cross-links forming a stem-loop macrocycle. Furthermore, an unusually stable aspartimide moiety is found within the loop macrocycle. We fully reconstituted fuscimiditide biosynthesis in vitro including formation of the ester and aspartimide moieties. The aspartimide moiety embedded in fuscimiditide hydrolyses regioselectively to isoaspartate. Surprisingly, this isoaspartate-containing peptide is also a substrate for the L-isoaspartyl methyltransferase homologue, thus driving any hydrolysis products back to the aspartimide form. Whereas an aspartimide is often considered a nuisance product in protein formulations, our data suggest that some RiPPs have aspartimide residues intentionally installed via enzymatic activity.
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Affiliation(s)
- Hader E Elashal
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Joseph D Koos
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Wai Ling Cheung-Lee
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Brian Choi
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Li Cao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Michelle A Richardson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Heather L White
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - A James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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9
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Heterologous Expression of Thermotolerant α-Glucosidase in Bacillus subtilis 168 and Improving Its Thermal Stability by Constructing Cyclized Proteins. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8100498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
α-glucosidase is an essential enzyme for the production of isomaltooligosaccharides (IMOs). Allowing α-glucosidase to operate at higher temperatures (above 60 °C) has many advantages, including reducing the viscosity of the reaction solution, enhancing the catalytic reaction rate, and achieving continuous production of IMOs. In the present study, the thermal stability of α-glucosidase was significantly improved by constructing cyclized proteins. We screened a thermotolerant α-glucosidase (AGL) with high transglycosylation activity from Thermoanaerobacter ethanolicus JW200 and heterologously expressed it in Bacillus subtilis 168. After forming the cyclized α-glucosidase by different isopeptide bonds (SpyTag/SpyCatcher, SnoopTag/SnoopCatcher, SdyTag/SdyCatcher, RIAD/RIDD), we determined the enzymatic properties of cyclized AGL. The optimal temperature of all cyclized AGL was increased by 5 °C, and their thermal stability was generally improved, with SpyTag-AGL-SpyCatcher having a 1.74-fold increase compared to the wild-type. The results of molecular dynamics simulations showed that the RMSF values of cyclized AGL decreased, indicating that the rigidity of the cyclized protein increased. This study provides an efficient method for improving the thermal stability of α-glucosidase.
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10
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Wu WH, Guo J, Zhang L, Zhang WB, Gao W. Peptide/protein-based macrocycles: from biological synthesis to biomedical applications. RSC Chem Biol 2022; 3:815-829. [PMID: 35866174 PMCID: PMC9257627 DOI: 10.1039/d1cb00246e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/08/2022] [Indexed: 11/21/2022] Open
Abstract
Living organisms have evolved cyclic or multicyclic peptides and proteins with enhanced stability and high bioactivity superior to their linear counterparts for diverse purposes. Herein, we review recent progress in applying this concept to artificial peptides and proteins to exploit the functional benefits of these macrocycles. Not only have simple cyclic forms been prepared, numerous macrocycle variants, such as knots and links, have also been developed. The chemical tools and synthetic strategies are summarized for the biological synthesis of these macrocycles, demonstrating it as a powerful alternative to chemical synthesis. Its further application to therapeutic peptides/proteins has led to biomedicines with profoundly improved pharmaceutical performances. Finally, we present our perspectives on the field and its future developments.
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Affiliation(s)
- 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
| | - Jianwen Guo
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
| | - Longshuai Zhang
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
| | - 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
| | - Weiping Gao
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
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11
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Engineering and exploiting synthetic allostery of NanoLuc luciferase. Nat Commun 2022; 13:789. [PMID: 35145068 PMCID: PMC8831504 DOI: 10.1038/s41467-022-28425-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/25/2022] [Indexed: 02/08/2023] Open
Abstract
Allostery enables proteins to interconvert different biochemical signals and form complex metabolic and signaling networks. We hypothesize that circular permutation of proteins increases the probability of functional coupling of new N- and C- termini with the protein's active center through increased local structural disorder. To test this we construct a synthetically allosteric version of circular permutated NanoLuc luciferase that can be activated through ligand-induced intramolecular non-covalent cyclisation. This switch module is tolerant of the structure of binding domains and their ligands, and can be used to create biosensors of proteins and small molecules. The developed biosensors covers a range of emission wavelengths and displays sensitivity as low as 50pM and dynamic range as high as 16-fold and could quantify their cognate ligand in human fluids. We apply hydrogen exchange kinetic mass spectroscopy to analyze time resolved structural changes in the developed biosensors and observe ligand-mediated folding of newly created termini.
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12
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Haim A, Neubacher S, Grossmann TN. Protein Macrocyclization for Tertiary Structure Stabilization. Chembiochem 2021; 22:2672-2679. [PMID: 34060202 PMCID: PMC8453710 DOI: 10.1002/cbic.202100111] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/26/2021] [Indexed: 12/30/2022]
Abstract
Proteins possess unique molecular recognition capabilities and enzymatic activities, features that are usually tied to a particular tertiary structure. To make use of proteins for biotechnological and biomedical purposes, it is often required to enforce their tertiary structure in order to ensure sufficient stability under the conditions inherent to the application of interest. The introduction of intramolecular crosslinks has proven efficient in stabilizing native protein folds. Herein, we give an overview of methods that allow the macrocyclization of expressed proteins, discussing involved reaction mechanisms and structural implications.
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Affiliation(s)
- Anissa Haim
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
- Incircular B.V.De Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Tom N. Grossmann
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
- Amsterdam Institute of Molecular and Life SciencesVU University AmsterdamAmsterdamThe Netherlands
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13
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Ree BJ, Satoh Y, Isono T, Satoh T. Highly Ordered Nanoscale Film Morphologies of Block Copolymers Governed by Nonlinear Topologies. ACS Macro Lett 2021; 10:811-818. [PMID: 35549184 DOI: 10.1021/acsmacrolett.1c00204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Among many properties of cyclic block copolymers, the notable domain spacing (d-spacing) reduction offers nonlinear topology as an effective tool for developing block copolymers for nanolithography. However, the current consensus regarding the topology-morphology correlation is ambiguous and in need of more studies. Here we present the morphological investigation on nanoscale films of cyclic and tadpole-shaped poly(n-decyl glycidyl ether-block-2-(2-(2-methoxyethoxy)ethoxy)ethyl glycidyl ether)s and their linear counterpart via synchrotron grazing-incidence X-ray scattering. All copolymers form phase-separated nanostructures, in which only the nonlinear copolymers form highly ordered and unidirectional nanostructures. Additionally, d-spacings of cyclic and tadpole-shaped block copolymers are 49.3-53.7% and 25.0-32.5% shorter than that of their linear counterpart, respectively, exhibiting greater or comparable d-spacing reductions against the experimentally and theoretically achieved values from the literature. Overall, this study demonstrates that cyclic and tadpole topologies can be utilized in developing materials with miniaturized dimensions, high structural ordering, and unidirectional orientation for various nanotechnology applications.
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Affiliation(s)
- Brian J. Ree
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Yusuke Satoh
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Takuya Isono
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Toshifumi Satoh
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
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14
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Hayes HC, Luk LYP, Tsai YH. Approaches for peptide and protein cyclisation. Org Biomol Chem 2021; 19:3983-4001. [PMID: 33978044 PMCID: PMC8114279 DOI: 10.1039/d1ob00411e] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/01/2021] [Indexed: 12/26/2022]
Abstract
The cyclisation of polypeptides can play a crucial role in exerting biological functions, maintaining stability under harsh conditions and conferring proteolytic resistance, as demonstrated both in nature and in the laboratory. To date, various approaches have been reported for polypeptide cyclisation. These approaches range from the direct linkage of N- and C- termini to the connection of amino acid side chains, which can be applied both in reaction vessels and in living systems. In this review, we categorise the cyclisation approaches into chemical methods (e.g. direct backbone cyclisation, native chemical ligation, aldehyde-based ligations, bioorthogonal reactions, disulphide formation), enzymatic methods (e.g. subtiligase variants, sortases, asparaginyl endopeptidases, transglutaminases, non-ribosomal peptide synthetases) and protein tags (e.g. inteins, engineered protein domains for isopeptide bond formation). The features of each approach and the considerations for selecting an appropriate method of cyclisation are discussed.
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Affiliation(s)
- Heather C Hayes
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT.
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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15
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16
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Zhang J, Yuan J, Li Z, Fu C, Xu M, Yang J, Jiang X, Zhou B, Ye X, Xu C. Exploring and exploiting plant cyclic peptides for drug discovery and development. Med Res Rev 2021; 41:3096-3117. [PMID: 33599316 DOI: 10.1002/med.21792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 01/10/2021] [Accepted: 01/31/2021] [Indexed: 01/07/2023]
Abstract
Ever since the discovery of insulin, natural peptides have become an important resource for therapeutic development. Decades of research has led to the discovery of a long list of peptide drugs with broad applications in clinics, from antibiotics to hypertension treatment to pain management. Many of these US FDA-approved peptide drugs are derived from microorganisms and animals. By contrast, the great potential of plant cyclic peptides as therapeutics remains largely unexplored. These macrocyclic peptides typically have rigid structures, good bioavailability and membrane permeability, making them appealing candidates for drug development and engineering. In this review, we introduce the three major classes of plant cyclic peptides and summarize their potential medical applications. We discuss how we can leverage the genome information of many different plants to quickly search for new cyclic peptides and how we can take advantage of the insights gained from their biosynthetic pathways to transform the process of production and drug development. These recent developments have provided a new angle for exploring and exploiting plant cyclic peptides, and we believe that many more peptide drugs derived from plants are about to come.
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Affiliation(s)
- Jingjing Zhang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong, China
| | - Jimin Yuan
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Zhijie Li
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Chunjin Fu
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Menglong Xu
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jing Yang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Xin Jiang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Boping Zhou
- Department of Infectious Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Xiufeng Ye
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Chengchao Xu
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
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17
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Wang R, Sun F. The Spy that links: Creation of nonlinear protein architectures and materials using SpyTag/SpyCatcher chemistry. Methods Enzymol 2020; 647:283-301. [PMID: 33482993 DOI: 10.1016/bs.mie.2020.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The peptide/protein pair, SpyTag/SpyCatcher, which is derived from split immunoglobulin-like collagen adhesin domain (CnaB2) from Streptococcus pyogenes, can spontaneously form a stable Lys-Asp isopeptide bond under physiological conditions. This enabling technology- also known as genetically encoded click chemistry owing to its marked efficiency and specificity-has led to a variety of applications in protein engineering, materials science and synthetic biology in recent years. In this chapter, we discuss the use of SpyTag/SpyCatcher chemistry to create nonlinear protein architectures and materials, with emphasis on its role in shaping up topology engineering as an emerging branch of protein engineering. The synthesis of entirely protein-based molecular networks, Spy networks, is highlighted. The protocols for preparing Spy networks and applications thereof are also illustrated.
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Affiliation(s)
- Ri Wang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, People's Republic of China
| | - Fei Sun
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, People's Republic of China.
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18
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Zhang F, Zhang W. Encrypting Chemical Reactivity in Protein Sequences toward
Information‐Coded
Reactions
†. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000083] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- 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 China
| | - 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 China
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Abstract
This Review explores the class of plant-derived macrocyclic peptides called cyclotides. We include an account of their discovery, characterization, and distribution in the plant kingdom as well as a detailed analysis of their sequences and structures, biosynthesis and chemical synthesis, biological functions, and applications. These macrocyclic peptides are around 30 amino acids in size and are characterized by their head-to-tail cyclic backbone and cystine knot motif, which render them to be exceptionally stable, with resistance to thermal or enzymatic degradation. Routes to their chemical synthesis have been developed over the past two decades, and this capability has facilitated a wide range of mutagenesis and structure-activity relationship studies. In turn, these studies have both led to an increased understanding of their mechanisms of action as well as facilitated a range of applications in agriculture and medicine, as ecofriendly crop protection agents, and as drug leads or scaffolds for pharmaceutical design. Our overall objective in this Review is to provide readers with a comprehensive overview of cyclotides that we hope will stimulate further work on this fascinating family of peptides.
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Affiliation(s)
- Simon J de Veer
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Meng-Wei Kan
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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20
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Zheng W, Zhou T, Li J, Jiang W, Zhang J, Xiao C, Wei D, Yang C, Xu R, Gong A, Zhang C, Bi Y. The Biosynthesis of Heterophyllin B in Pseudostellaria heterophylla From prePhHB-Encoded Precursor. FRONTIERS IN PLANT SCIENCE 2019; 10:1259. [PMID: 31749814 PMCID: PMC6842982 DOI: 10.3389/fpls.2019.01259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Plant cyclic peptides (CPs) are a large group of small molecule metabolites found in a wide variety of plants, including traditional Chinese medicinal plants. However, the majority of plant CPs have not been studied for their biosynthetic mechanisms, including heterophyllin B (HB), which is one of the characteristic chemical components of Pseudostellaria heterophylla. Here, we screened the precursor gene (prePhHB) of HB in P. heterophylla and functionally identified its correctness in vivo and in vitro. First, we developed a new method to screen the precursors of HB from 16 candidate linear peptides. According to transcriptome sequencing data, we cloned the genes that encoded the HB precursor peptides and confirmed that the prePhHB-encoded precursor peptide could enzymatically synthesize HB. Next, we generated the transgenic tobacco that expressed prePhHB, and the results showed that HB was detected in transgenic tobacco. Moreover, we revealed that prePhHB gene expression is positively correlated with HB accumulation in P. heterophylla. Mutations in the prePhHB gene may influence the accumulation of HB in P. heterophylla. These results suggest that HB is ribosomally synthesized and posttranslationally modified peptide (RiPP) derived from the precursor gene prePhHB-encoded precursor peptide, and the core peptide sequence of HB is IFGGLPPP in P. heterophylla. This study developed a new idea for the rapid identification of Caryophyllaceae-type CP precursor peptides via RNA-sequencing data mining.
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Affiliation(s)
- Wei Zheng
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Tao Zhou
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jun Li
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Weike Jiang
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jinqiang Zhang
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Chenghong Xiao
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Dequn Wei
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Changgui Yang
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Rong Xu
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Anhui Gong
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Chen Zhang
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yan Bi
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
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21
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Ojeda PG, Cardoso MH, Franco OL. Pharmaceutical applications of cyclotides. Drug Discov Today 2019; 24:2152-2161. [PMID: 31541712 DOI: 10.1016/j.drudis.2019.09.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/05/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023]
Abstract
Cyclotides are cyclic peptides, present in several plant families, that show diverse biological properties. Structurally, cyclotides share a distinctive head-to-tail circular knotted topology of three disulfide bonds. This framework provides cyclotides with extraordinary resistance to thermal and chemical denaturation. There is increasing interest in the therapeutic potential of cyclotides, which combine several promising pharmaceutical properties, including binding affinity, target selectivity, and low toxicity towards healthy mammalian cells. Recently, cyclotides have been reported to be orally bioavailable and have proved to be amenable to modifications. Here, we provide an overview of the structure, properties, and pharmaceutical applications of cyclotides.
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Affiliation(s)
- Paola G Ojeda
- Escuela de Química y Farmacia, Facultad de Medicina, Universidad Católica del Maule, Av. San Miguel 3605, Talca 3480112, Chile
| | - Marlon H Cardoso
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil; 3S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Octávio L Franco
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil; 3S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.
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22
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Franke B, Mylne JS, Rosengren KJ. Buried treasure: biosynthesis, structures and applications of cyclic peptides hidden in seed storage albumins. Nat Prod Rep 2019; 35:137-146. [PMID: 29379937 DOI: 10.1039/c7np00066a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Covering: 1999 up to the end of 2017The small cyclic peptide SunFlower Trypsin Inhibitor-1 (SFTI-1) from sunflower seeds is the prototypic member of a novel family of natural products. The biosynthesis of these peptides is intriguing as their gene-encoded peptide backbone emerges from a precursor protein that also contains a seed storage albumin. The peptide sequence is cleaved out from the precursor and cyclised by the albumin-maturing enzymatic machinery. Three-dimensional solution NMR structures of a number of these peptides, and of the intact precursor protein preproalbumin with SFTI-1, have now been elucidated. Furthermore, the evolution of the family has been described and a detailed understanding of the biosynthetic steps, which are necessary to produce cyclic SFTI-1, is emerging. Macrocyclisation provides peptide stability and thus represents a key strategy in peptide drug development. Consequently the constrained structure of SFTI-1 has been explored as a template for protein engineering, for tuning selectivity towards clinically relevant proteases and for grafting in sequences with completely novel functions. Here we review the discovery of the SFTI-1 peptide family, their evolution, biosynthetic origin, and structural features, as well as highlight the potential applications of this unique class of natural products.
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Affiliation(s)
- B Franke
- The University of Queensland, Faculty of Medicine, School of Biomedical Sciences, Brisbane, QLD 4072, Australia.
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23
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Gao DY, Sun XB, Liu MQ, Liu YN, Zhang HE, Shi XL, Li YN, Wang JK, Yin SJ, Wang Q. Characterization of Thermostable and Chimeric Enzymes via Isopeptide Bond-Mediated Molecular Cyclization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:6837-6846. [PMID: 31180217 DOI: 10.1021/acs.jafc.9b01459] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Mannooligosaccharides are released by mannan-degrading endo-β-1,4-mannanase and are known as functional additives in human and animal diets. To satisfy demands for biocatalysis and bioprocessing in crowed environments, in this study, we employed a recently developed enzyme-engineering system, isopeptide bond-mediated molecular cyclization, to modify a mesophilic mannanase from Bacillus subtilis. The results revealed that the cyclized enzymes showed enhanced thermostability and ion stability and resilience to aggregation and freeze-thaw treatment by maintaining their conformational structures. Additionally, by using the SpyTag/SpyCatcher system, we generated a mannanase-xylanase bifunctional enzyme that exhibited a synergistic activity in substrate deconstruction without compromising substrate affinity. Interestingly, the dual-enzyme ring conformation was observed to be more robust than the linear enzyme but inferior to the single-enzyme ring conformation. Taken together, these findings provided new insights into the mechanisms of molecular cyclization on stability improvement and will be useful in the production of new functional oligosaccharides and feed additives.
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Affiliation(s)
- De-Ying Gao
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Xiao-Bao Sun
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Ming-Qi Liu
- National and Local United Engineering Lab of Quality Controlling Technology and Instrumentation for Marine Food, College of Life Science , China Jiliang University , Hangzhou 310018 , Zhejiang , China
| | - Yan-Ni Liu
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Hui-En Zhang
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Xin-Lei Shi
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Yang-Nan Li
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Jia-Kun Wang
- College of Animal Science , Zhejiang University , Hangzhou 310058 , Zhejiang , China
| | - Shang-Jun Yin
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Qian Wang
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
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24
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Genome mining for ribosomally synthesised and post-translationally modified peptides (RiPPs) reveals undiscovered bioactive potentials of actinobacteria. Antonie van Leeuwenhoek 2019; 112:1477-1499. [DOI: 10.1007/s10482-019-01276-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/14/2019] [Indexed: 01/22/2023]
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25
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Du J, Chan LY, Poth AG, Craik DJ. Discovery and Characterization of Cyclic and Acyclic Trypsin Inhibitors from Momordica dioica. JOURNAL OF NATURAL PRODUCTS 2019; 82:293-300. [PMID: 30673219 DOI: 10.1021/acs.jnatprod.8b00716] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Momordica trypsin inhibitors (TIs) such as those isolated from the seeds of the gấc fruit, Momordica cochinchinensis (MCoTI-I and MCoTI-II), are widely used as scaffolds for drug design studies. To more effectively exploit these molecules in the development of therapeutics, there is a need for wider discovery of the natural sequence diversity among TIs from other species in the Momordica subfamily. Here we report the discovery of the encoding gene and six TIs from the seeds of the spiny gourd, Momordica dioica, four of which possess novel sequences (Modi 1, 3, 5, and 6) and two (Modi 2 and 4) of which are known peptides (TI-14, TI-17) previously identified in Momordica subangulata. Modi 6 is an acyclic peptide featuring a pyrrolidone carboxylic acid modification, whereas the remaining five TIs are cyclic. All Modi peptides display similar overall structures and trypsin inhibitory activities. No toxicity was observed for these peptides when tested against cancer and insect cells. All Modi peptides were exceptionally stable over 24 h in human serum, indicating a dual strategy to stabilize the peptides in nature, either head-to-tail cyclization or N-pyrolation, which suggests these peptides might be excellent candidates as scaffolds for epitope stabilization in drug design studies.
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Affiliation(s)
- Junqiao Du
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Lai Yue Chan
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Aaron G Poth
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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26
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Zhang RY, Thapa P, Espiritu MJ, Menon V, Bingham JP. From nature to creation: Going around in circles, the art of peptide cyclization. Bioorg Med Chem 2018; 26:1135-1150. [DOI: 10.1016/j.bmc.2017.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/06/2017] [Accepted: 11/09/2017] [Indexed: 02/02/2023]
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27
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28
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van Heel AJ, Montalban-Lopez M, Oliveau Q, Kuipers OP. Genome-guided identification of novel head-to-tail cyclized antimicrobial peptides, exemplified by the discovery of pumilarin. Microb Genom 2017; 3:e000134. [PMID: 29177092 PMCID: PMC5695211 DOI: 10.1099/mgen.0.000134] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 09/01/2017] [Indexed: 11/18/2022] Open
Abstract
The need for novel antibiotics in an era where antimicrobial resistance is on the rise, and the number of new approved antimicrobial drugs reaching the market is declining, is evident. The underused potential of post-translationally modified peptides for clinical use makes this class of peptides interesting candidates. In this study, we made use of the vast amounts of available genomic data and screened all publicly available prokaryotic genomes (~3000) to identify 394 novel head-to-tail cyclized antimicrobial peptides. To verify these in silico results, we isolated and characterized a novel antimicrobial peptide from Bacillus pumilus that we named pumilarin. Pumilarin was demonstrated to have a circular structure and showed antimicrobial activity against several indicator strains, including pathogens.
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Affiliation(s)
- Auke J van Heel
- 1Molecular Genetics, University of Groningen, Groningen, Nijenborgh 7, NA 9747 AG, The Netherlands
| | - Manuel Montalban-Lopez
- 1Molecular Genetics, University of Groningen, Groningen, Nijenborgh 7, NA 9747 AG, The Netherlands.,2Department of Microbiology, University of Granada, Granada, Spain
| | - Quentin Oliveau
- 1Molecular Genetics, University of Groningen, Groningen, Nijenborgh 7, NA 9747 AG, The Netherlands
| | - Oscar P Kuipers
- 1Molecular Genetics, University of Groningen, Groningen, Nijenborgh 7, NA 9747 AG, The Netherlands
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29
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Mamo G. Anaerobes as Sources of Bioactive Compounds and Health Promoting Tools. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 156:433-464. [PMID: 27432247 DOI: 10.1007/10_2016_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aerobic microorganisms have been sources of medicinal agents for several decades and an impressive variety of drugs have been isolated from their cultures, studied and formulated to treat or prevent diseases. On the other hand, anaerobes, which are believed to be the oldest life forms on earth and evolved remarkably diverse physiological functions, have largely been neglected as sources of bioactive compounds. However, results obtained from the limited research done so far show that anaerobes are capable of producing a range of interesting bioactive compounds that can promote human health. In fact, some of these bioactive compounds are found to be novel in their structure and/or mode of action.Anaerobes play health-promoting roles through their bioactive products as well as application of whole cells. The bioactive compounds produced by these microorganisms include antimicrobial agents and substances such as immunomodulators and vitamins. Bacteriocins produced by anaerobes have been in use as preservatives for about 40 years. Because these substances are effective at low concentrations, encounter relatively less resistance from bacteria and are safe to use, there is a growing interest in these antimicrobial agents. Moreover, several antibiotics have been reported from the cultures of anaerobes. Closthioamide and andrimid produced by Clostridium cellulolyticum and Pantoea agglomerans, respectively, are examples of novel antibiotics of anaerobe origin. The discovery of such novel bioactive compounds is expected to encourage further studies which can potentially lead to tapping of the antibiotic production potential of this fascinating group of microorganisms.Anaerobes are widely used in preparation of fermented foods and beverages. During the fermentation processes, these organisms produce a number of bioactive compounds including anticancer, antihypertensive and antioxidant substances. The well-known health promoting effect of fermented food is mostly due to these bioactive compounds. In addition to their products, whole cell anaerobes have very interesting applications for enhancing the quality of life. Probiotic anaerobes have been on the market for many years and are receiving growing acceptance as health promoters. Gut anaerobes have been used to treat patients suffering from severe Clostridium difficile infection syndromes including diarrhoea and colitis which cannot be treated by other means. Whole cell anaerobes are also studied to detect and cure cancer. In recent years, evidence is emerging that anaerobes constituting the microbiome are linked to our overall health. A dysfunctional microbiome is believed to be the cause of many diseases including cancer, allergy, infection, obesity, diabetes and several other disorders. Maintaining normal microflora is believed to alleviate some of these serious health problems. Indeed, the use of probiotics and prebiotics which favourably change the number and composition of the gut microflora is known to render a health promoting effect. Our interaction with the microbiome anaerobes is complex. In fact, not only our lives but also our identities are more closely linked to the anaerobic microbial world than we may possibly imagine. We are just at the beginning of unravelling the secret of association between the microbiome and human body, and a clear understanding of the association may bring a paradigm shift in the way we diagnose and treat diseases and disorders. This chapter highlights some of the work done on bioactive compounds and whole cell applications of the anaerobes that foster human health and improve the quality of life.
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Affiliation(s)
- Gashaw Mamo
- Biotechnology, Center for Chemistry & Chemical Engineering, Lund University, 221 00, Lund, Sweden.
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30
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Strzelecka P, Czaplinska D, Sadej R, Wardowska A, Pikula M, Lesner A. Simplified, serine-rich theta-defensin analogues as antitumour peptides. Chem Biol Drug Des 2017; 90:52-63. [PMID: 28004513 DOI: 10.1111/cbdd.12927] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/05/2016] [Accepted: 12/10/2016] [Indexed: 01/15/2023]
Abstract
θ-defensins belong to the family of host defence peptides. They are the only known example of cyclic polypeptides in animal proteomes. This study presents the synthesis of simplified θ-defensin analogues with pairs of cysteine replaced either by alanine, leucine or serine residues. Cytotoxicity tests were performed on human mammary epithelial (HB2) and breast cancer (SKBR3, MDA-MB-231) cell lines to determine whether peptides are selectively targeting cancer cells. The effect of these peptides was also evaluated in 3D Matrigel cultures, which are based on extracellular matrix components and therefore closely represent in vivo conditions. Finally, to determine whether analogues are able to sensitize MDA-MB-231 triple-negative breast cancer cells to chemotherapeutics, we co-administrated peptides with cisplatin or doxorubicin hydrochloride also in 3D Matrigel cultures. Additionally, cytotoxicity towards peripheral blood mononuclear cells and haemolytic effect were examined for a chosen representative of synthesized compounds. The results showed that positively charged serine-containing θ-defensin derivatives were more cytotoxic towards breast cancer cells (SKBR3, MDA-MB-231) than towards mammary epithelial cells (HB2). Analogues enhanced the effect of cisplatin and doxorubicin hydrochloride on triple-negative breast cancer cell line (MDA-MB-231).
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Affiliation(s)
- Paulina Strzelecka
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Dominika Czaplinska
- Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Rafal Sadej
- Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Anna Wardowska
- Department of Clinical Immunology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Michal Pikula
- Department of Clinical Immunology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Adam Lesner
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
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Schrimpf A, Linne U, Geyer A. Eight at one stroke – a synthetic tetra-disulfide peptide epitope. Org Biomol Chem 2017; 15:2512-2521. [DOI: 10.1039/c6ob02746f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A tetra-disulfide peptide dimer, representing an antiparallel hinge, is synthesised without the need for orthogonal cysteine protecting groups.
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Affiliation(s)
- Andreas Schrimpf
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Uwe Linne
- Mass spectrometry facility of the Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Armin Geyer
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
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32
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Koehbach J, Clark RJ. Unveiling the diversity of cyclotides by combining peptidome and transcriptome analysis. Biopolymers 2016; 106:774-783. [DOI: 10.1002/bip.22858] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/05/2016] [Accepted: 04/11/2016] [Indexed: 01/11/2023]
Affiliation(s)
- Johannes Koehbach
- School of Biomedical Sciences; The University of Queensland; 4072 St. Lucia QLD Australia
| | - Richard J. Clark
- School of Biomedical Sciences; The University of Queensland; 4072 St. Lucia QLD Australia
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Rabideau AE, Pentelute BL. A d-Amino Acid at the N-Terminus of a Protein Abrogates Its Degradation by the N-End Rule Pathway. ACS CENTRAL SCIENCE 2015; 1:423-430. [PMID: 26807441 PMCID: PMC4711398 DOI: 10.1021/acscentsci.5b00308] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Indexed: 06/05/2023]
Abstract
Eukaryotes have evolved the ubiquitin (Ub)/proteasome system to degrade polypeptides. The Ub/proteasome system is one way that cells regulate cytosolic protein and amino acids levels through the recognition and ubiquitination of a protein's N-terminus via E1, E2, and E3 enzymes. The process by which the N-terminus stimulates intracellular protein degradation is referred to as the N-end rule. Characterization of the N-end rule has been limited to only the natural l-amino acids. Using a cytosolic delivery platform derived from anthrax lethal toxin, we probed the stability of mixed chirality proteins, containing one d-amino acid on the N-terminus of otherwise all l-proteins. In all cases, we observed that one N-terminal d-amino acid stabilized the cargo protein to proteasomal degradation with respect to the N-end rule. We found that since the mixed chirality proteins were not polyubiquitinated, they evaded N-end-mediated proteasomal degradation. Evidently, a subtle change on the N-terminus of a natural protein can enhance its intracellular lifetime.
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Haglund E. Engineering covalent loops in proteins can serve as an on/off switch to regulate threaded topologies. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354107. [PMID: 26291088 DOI: 10.1088/0953-8984/27/35/354107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Knots in proteins are under active investigation motivating refinements of current techniques and the development of tools to better understand the knotted topology. A strong focus is to identify new knots and expand upon the current understanding of their complex topology. Previous work has shown that the knotted topology, even in the simplest case of knots, encompasses a variety of unique challenges in folding and tying a chain. To bypass many of the in vitro experimental complications involved in working with knots, it is useful to apply methodologies to a more simplified system. The pierced lasso bundles (PLB), we discovered where a single disulphide bridge holds the threaded topology together, presents a simpler system to study knots in vitro. Having a disulphide bridge as an on/off switch between the threaded/unthreaded topology is advantageous because a covalent loop allows manipulation of the knot without directly altering affecting secondary and tertiary structure. Because disulphide bridges are commonly used in protein engineering, a pierced lasso (PL) topology can be easily introduced into a protein of interest to form a knotted topology within a given secondary structure. It is also important to take into account that if formed, disulphides can inadvertently introduce an unwanted PL. This was found upon determination of the crystal structure (PDB code 2YHG) of the recently de novo designed nucleoside hydrolase. Our detailed investigations of the PL presented here will allow researchers to look at the introduction of disulphide bridges in a larger context with respect to potential geometrical consequences on the structure and functional properties of proteins.
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Affiliation(s)
- Ellinor Haglund
- Center for Theoretical Biological Physics (CTBP) and Department of Physics, University of California, San Diego (UCSD), La Jolla, CA 92093, USA. Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
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35
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Waldhauer MC, Schmitz SN, Ahlmann-Eltze C, Gleixner JG, Schmelas CC, Huhn AG, Bunne C, Büscher M, Horn M, Klughammer N, Kreft J, Schäfer E, Bayer PA, Krämer SG, Neugebauer J, Wehler P, Mayer MP, Eils R, Di Ventura B. Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation. MOLECULAR BIOSYSTEMS 2015; 11:3231-43. [DOI: 10.1039/c5mb00341e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While using a serine (S) as linker for circularization increases the thermostability, a longer linker (RGKCWE) leads to reduced aggregation after heat shock at elevated temperatures.
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36
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Duffy FJ, Devocelle M, Croucher DR, Shields DC. Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions. BMC Bioinformatics 2014; 15:305. [PMID: 25231912 PMCID: PMC4262234 DOI: 10.1186/1471-2105-15-305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 07/17/2014] [Indexed: 01/04/2023] Open
Abstract
Background Bioactive cyclic peptides derived from natural sources are well studied, particularly those derived from non-ribosomal synthetases in fungi or bacteria. Ribosomally synthesised bioactive disulphide-bonded loops represent a large, naturally enriched library of potential bioactive compounds, worthy of systematic investigation. Results We examined the distribution of short cyclic loops on the surface of a large number of proteins, especially membrane or extracellular proteins. Available three-dimensional structures highlighted a number of disulphide-bonded loops responsible for the majority of the likely binding interactions in a variety of protein complexes, due to their location at protein-protein interfaces. We find that disulphide-bonded loops at protein-protein interfaces may, but do not necessarily, show biological activity independent of their parent protein. Examining the conservation of short disulphide bonded loops in proteins, we find a small but significant increase in conservation inside these loops compared to surrounding residues. We identify a subset of these loops that exhibit a high relative conservation, particularly among peptide hormones. Conclusions We conclude that short disulphide-bonded loops are found in a wide variety of biological interactions. They may retain biological activity outside their parent proteins. Such structurally independent peptides may be useful as biologically active templates for the development of novel modulators of protein-protein interactions. Electronic supplementary material The online version of this article (doi:10.1186/1471-2105-15-305) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Denis C Shields
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland.
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Butelase 1 is an Asx-specific ligase enabling peptide macrocyclization and synthesis. Nat Chem Biol 2014; 10:732-8. [PMID: 25038786 DOI: 10.1038/nchembio.1586] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 06/13/2014] [Indexed: 01/29/2023]
Abstract
Proteases are ubiquitous in nature, whereas naturally occurring peptide ligases, enzymes catalyzing the reverse reactions of proteases, are rare occurrences. Here we describe the discovery of butelase 1, to our knowledge the first asparagine/aspartate (Asx) peptide ligase to be reported. This highly efficient enzyme was isolated from Clitoria ternatea, a cyclic peptide-producing medicinal plant. Butelase 1 shares 71% sequence identity and the same catalytic triad with legumain proteases but does not hydrolyze the protease substrate of legumain. Instead, butelase 1 cyclizes various peptides of plant and animal origin with yields greater than 95%. With Kcat values of up to 17 s(-1) and catalytic efficiencies as high as 542,000 M(-1) s(-1), butelase 1 is the fastest peptide ligase known. Notably, butelase 1 also displays broad specificity for the N-terminal amino acids of the peptide substrate, thus providing a new tool for C terminus-specific intermolecular peptide ligations.
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38
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39
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Craik DJ, Malik U. Cyclotide biosynthesis. Curr Opin Chem Biol 2013; 17:546-54. [PMID: 23809361 DOI: 10.1016/j.cbpa.2013.05.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
Abstract
Cyclotides are bioactive macrocyclic peptides from plants that are characterized by their exceptional stability and potential applications as protein engineering or drug design frameworks. Their stability arises from their unique cyclic cystine knot structure, which combines a head-to-tail cyclic peptide backbone with three conserved disulfide bonds having a knotted topology. Cyclotides are ribosomally synthesized by plants and expressed in a wide range of tissues, including leaves, flowers, stems and roots. Here we describe recent studies that have examined the biosynthesis of cyclotides and in particular the mechanism associated with post-translational backbone cyclization.
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Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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40
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Abstract
The suite of currently used drugs can be divided into two categories - traditional 'small molecule' drugs with typical molecular weights of <500 Da but with oral bioavailability, and much larger 'biologics' typically >5000 Da that are not orally bioavailable and need to be delivered via injection. Due to their small size, conventional small molecule drugs may suffer from reduced target selectivity that often ultimately manifests in human side-effects, whereas protein therapeutics tend to be exquisitely specific for their targets due to many more interactions with them, but this comes at a cost of low bioavailability, poor membrane permeability, and metabolic instability. The time has now come to reinvestigate new drug leads that fit between these two molecular weight extremes, with the goal of combining advantages of small molecules (cost, conformational restriction, membrane permeability, metabolic stability, oral bioavailability) with those of proteins (natural components, target specificity, high potency). This article uses selected examples of peptides to highlight the importance of peptide drugs, some potential new opportunities for their exploitation, and some difficult challenges ahead in this field.
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Affiliation(s)
- David J Craik
- Division of Chemistry & Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia.
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41
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Kedarisetti P, Mizianty MJ, Kaas Q, Craik DJ, Kurgan L. Prediction and characterization of cyclic proteins from sequences in three domains of life. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:181-90. [PMID: 23669569 DOI: 10.1016/j.bbapap.2013.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 04/12/2013] [Accepted: 05/02/2013] [Indexed: 01/04/2023]
Abstract
Cyclic proteins (CPs) have circular chains with a continuous cycle of peptide bonds. Their unique structural traits result in greater stability and resistance to degradation when compared to their acyclic counterparts. They are also promising targets for pharmaceutical/therapeutic applications. To date, only a few hundred CPs are known, although recent studies suggest that their numbers might be substantially higher. Here we developed a first-of-its-kind, accurate and high-throughput method called CyPred that predicts whether a given protein chain is cyclic. CyPred considers currently well-represented CP families: cyclotides, cyclic defensins, bacteriocins, and trypsin inhibitors. Empirical tests demonstrate that CyPred outperforms commonly used alignment methods. We used CyPred to estimate the incidence of CPs and found ~3500 putative CPs among 5.7+ million chains from 642 fully sequenced proteomes from archaea, bacteria, and eukaryotes. The median number of putative CPs per species ranges from three for archaea proteomes to two for eukaryotes/bacteria, with 7% of archaea, 11% of bacterial, and 16% of eukaryotic proteomes having 10+ CPs. The differences in the estimated fractions of CPs per proteome are as large as three orders of magnitude. Among eukaryotes, animals have higher ratios of CPs compared to fungi, while plants have the largest spread of the ratios. We also show that proteomes enriched in cyclic proteins evolve more slowly than proteomes with fewer cyclic chains. Our results suggest that further research is needed to fully uncover the scope and potential of cyclic proteins. A list of putative CPs and the CyPred method are available at http://biomine.ece.ualberta.ca/CyPred/. This article is part of a Special Issue entitled: Computational Proteomics, Systems Biology & Clinical Implications. Guest Editor: Yudong Cai.
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Affiliation(s)
- Pradyumna Kedarisetti
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada
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42
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Kaas Q, Craik DJ. NMR of plant proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:1-34. [PMID: 23611313 DOI: 10.1016/j.pnmrs.2013.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/21/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Quentin Kaas
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
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43
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Koehler KC, Alge DL, Anseth KS, Bowman CN. Development of a Maleimide Amino Acid for Use as a Tool for Peptide Conjugation and Modification. Int J Pept Res Ther 2013. [DOI: 10.1007/s10989-013-9347-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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44
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Barber CJS, Pujara PT, Reed DW, Chiwocha S, Zhang H, Covello PS. The two-step biosynthesis of cyclic peptides from linear precursors in a member of the plant family Caryophyllaceae involves cyclization by a serine protease-like enzyme. J Biol Chem 2013; 288:12500-10. [PMID: 23486480 DOI: 10.1074/jbc.m112.437947] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Caryophyllaceae-type cyclic peptides (CPs) of 5-12 proteinogenic amino acids occur in 10 plant families. In Saponaria vaccaria (Caryophyllaceae), they have been shown to be formed from linear peptide precursors derived from ribosomal translation. There is also evidence for such precursors in other members of the Caryophyllaceae, Rutaceae, and Linaceae families. The biosynthesis of CP in the developing seeds of S. vaccaria was investigated with respect to the enzymes involved in precursor processing. Through biochemical assays with seed extracts and synthetic peptides, an enzyme named oligopeptidase 1 (OLP1) was found that catalyzes the cleavage of intermediates at the N terminus of the incipient CP. A second enzyme, peptide cyclase 1 (PCY1), which was separated chromatographically from OLP1, was found to act on the product of OLP1, giving rise to a cyclic peptide and concomitant removal of a C-terminal flanking sequence. PCY1 was partially purified, and using the methods of proteomics, a full-length cDNA clone encoding an enzyme matching the properties of PCY1 was obtained. The substrate specificity of purified recombinant PCY1, believed to be the first cloned plant enzyme whose function is peptide cyclization, was tested with synthetic peptides. The results are discussed in the light of CP biosynthetic systems of other organisms.
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Affiliation(s)
- Carla J S Barber
- National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
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45
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Jagadish K, Borra R, Lacey V, Majumder S, Shekhtman A, Wang L, Camarero JA. Expression of fluorescent cyclotides using protein trans-splicing for easy monitoring of cyclotide-protein interactions. Angew Chem Int Ed Engl 2013; 52:3126-31. [PMID: 23322720 PMCID: PMC3767473 DOI: 10.1002/anie.201209219] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Krishnappa Jagadish
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033, USA
| | - Radikha Borra
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033, USA
| | - Vanessa Lacey
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Subhabrata Majumder
- Department of Chemistry, State University of New York, Albany, NY 12222, USA
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York, Albany, NY 12222, USA
| | - Lei Wang
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90033, USA
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46
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Coluzza I, van Oostrum PDJ, Capone B, Reimhult E, Dellago C. Sequence controlled self-knotting colloidal patchy polymers. PHYSICAL REVIEW LETTERS 2013; 110:075501. [PMID: 25166382 DOI: 10.1103/physrevlett.110.075501] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Indexed: 06/03/2023]
Abstract
Knotted chains are a promising class of polymers with many applications for materials science and drug delivery. Here we introduce an experimentally realizable model for the design of chains with controllable topological properties. Recently, we have developed a systematic methodology to construct self-assembling chains of simple particles, with final structures fully controlled by the sequence of particles along the chain. The individual particles forming the chain are colloids decorated with mutually interacting patches, which can be manufactured in the laboratory with current technology. Our methodology is applied to the design of sequences folding into self-knotting chains, in which the end monomers are by construction always close together in space. The knotted structure can then be externally locked simply by controlling the interaction between the end monomers, paving the way to applications in the design and synthesis of active materials and novel carriers for drugs delivery.
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Affiliation(s)
- Ivan Coluzza
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Peter D J van Oostrum
- Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Barbara Capone
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Erik Reimhult
- Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
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Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian KD, Fischbach MA, Garavelli JS, Göransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Müller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJT, Rebuffat S, Ross RP, Sahl HG, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Süssmuth RD, Tagg JR, Tang GL, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 2013; 30:108-60. [PMID: 23165928 DOI: 10.1039/c2np20085f] [Citation(s) in RCA: 1445] [Impact Index Per Article: 131.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.
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Affiliation(s)
- Paul G Arnison
- Prairie Plant Systems Inc, Botanical Alternatives Inc, Suite 176, 8B-3110 8th Street E, Saskatoon, SK, S7H 0W2, Canada
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Izzo I, Ianniello G, De Cola C, Nardone B, Erra L, Vaughan G, Tedesco C, De Riccardis F. Structural Effects of Proline Substitution and Metal Binding on Hexameric Cyclic Peptoids. Org Lett 2013; 15:598-601. [DOI: 10.1021/ol3034143] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Irene Izzo
- Department of Chemistry and Biology, University of Salerno, Via Ponte don Melillo, 84084, Fisciano (SA), Italy, and European Synchrotron Radiation Facility, 8 Rue J. Horowitz, 38043 Grenoble, France
| | - Graziella Ianniello
- Department of Chemistry and Biology, University of Salerno, Via Ponte don Melillo, 84084, Fisciano (SA), Italy, and European Synchrotron Radiation Facility, 8 Rue J. Horowitz, 38043 Grenoble, France
| | - Chiara De Cola
- Department of Chemistry and Biology, University of Salerno, Via Ponte don Melillo, 84084, Fisciano (SA), Italy, and European Synchrotron Radiation Facility, 8 Rue J. Horowitz, 38043 Grenoble, France
| | - Brunello Nardone
- Department of Chemistry and Biology, University of Salerno, Via Ponte don Melillo, 84084, Fisciano (SA), Italy, and European Synchrotron Radiation Facility, 8 Rue J. Horowitz, 38043 Grenoble, France
| | - Loredana Erra
- Department of Chemistry and Biology, University of Salerno, Via Ponte don Melillo, 84084, Fisciano (SA), Italy, and European Synchrotron Radiation Facility, 8 Rue J. Horowitz, 38043 Grenoble, France
| | - Gavin Vaughan
- Department of Chemistry and Biology, University of Salerno, Via Ponte don Melillo, 84084, Fisciano (SA), Italy, and European Synchrotron Radiation Facility, 8 Rue J. Horowitz, 38043 Grenoble, France
| | - Consiglia Tedesco
- Department of Chemistry and Biology, University of Salerno, Via Ponte don Melillo, 84084, Fisciano (SA), Italy, and European Synchrotron Radiation Facility, 8 Rue J. Horowitz, 38043 Grenoble, France
| | - Francesco De Riccardis
- Department of Chemistry and Biology, University of Salerno, Via Ponte don Melillo, 84084, Fisciano (SA), Italy, and European Synchrotron Radiation Facility, 8 Rue J. Horowitz, 38043 Grenoble, France
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Jagadish K, Borra R, Lacey V, Majumder S, Shekhtman A, Wang L, Camarero JA. Expression of Fluorescent Cyclotides using Protein Trans-Splicing for Easy Monitoring of Cyclotide-Protein Interactions. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209219] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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