1
|
Majekodunmi T, Britton D, Montclare JK. Engineered Proteins and Materials Utilizing Residue-Specific Noncanonical Amino Acid Incorporation. Chem Rev 2024. [PMID: 39008623 DOI: 10.1021/acs.chemrev.3c00855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The incorporation of noncanonical amino acids into proteins and protein-based materials has significantly expanded the repertoire of available protein structures and chemistries. Through residue-specific incorporation, protein properties can be globally modified, resulting in the creation of novel proteins and materials with diverse and tailored characteristics. In this review, we highlight recent advancements in residue-specific incorporation techniques as well as the applications of the engineered proteins and materials. Specifically, we discuss their utility in bio-orthogonal noncanonical amino acid tagging (BONCAT), fluorescent noncanonical amino acid tagging (FUNCAT), threonine-derived noncanonical amino acid tagging (THRONCAT), cross-linking, fluorination, and enzyme engineering. This review underscores the importance of noncanonical amino acid incorporation as a tool for the development of tailored protein properties to meet diverse research and industrial needs.
Collapse
Affiliation(s)
- Temiloluwa Majekodunmi
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department of Biomedical Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
- Department of Chemistry, New York University, New York, New York 10012, United States
- Department of Biomaterials, New York University College of Dentistry, New York, New York 10010, United States
- Department of Radiology, New York University Langone Health, New York, New York 10016, United States
| |
Collapse
|
2
|
Gran-Scheuch A, Hanreich S, Keizer I, W Harteveld J, Ruijter E, Drienovská I. Designing Michaelases: exploration of novel protein scaffolds for iminium biocatalysis. Faraday Discuss 2024. [PMID: 38842386 DOI: 10.1039/d4fd00057a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Biocatalysis is becoming a powerful and sustainable alternative for asymmetric catalysis. However, enzymes are often restricted to metabolic and less complex reactivities. This can be addressed by protein engineering, such as incorporating new-to-nature functional groups into proteins through the so-called expansion of the genetic code to produce artificial enzymes. Selecting a suitable protein scaffold is a challenging task that plays a key role in designing artificial enzymes. In this work, we explored different protein scaffolds for an abiological model of iminium-ion catalysis, Michael addition of nitromethane into E-cinnamaldehyde. We studied scaffolds looking for open hydrophobic pockets and enzymes with described binding sites for the targeted substrate. The proteins were expressed and variants harboring functional amine groups - lysine, p-aminophenylalanine, or N6-(D-prolyl)-L-lysine - were analyzed for the model reaction. Among the newly identified scaffolds, a thermophilic ene-reductase from Thermoanaerobacter pseudethanolicus was shown to be the most promising biomolecular scaffold for this reaction.
Collapse
Affiliation(s)
- Alejandro Gran-Scheuch
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
| | - Stefanie Hanreich
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
| | - Iris Keizer
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
| | - Jaap W Harteveld
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
| | - Eelco Ruijter
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
| | - Ivana Drienovská
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
| |
Collapse
|
3
|
Agyemang E, Gonneville AN, Tiruvadi-Krishnan S, Lamichhane R. Exploring GPCR conformational dynamics using single-molecule fluorescence. Methods 2024; 226:35-48. [PMID: 38604413 PMCID: PMC11098685 DOI: 10.1016/j.ymeth.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are membrane proteins that transmit specific external stimuli into cells by changing their conformation. This conformational change allows them to couple and activate G-proteins to initiate signal transduction. A critical challenge in studying and inferring these structural dynamics arises from the complexity of the cellular environment, including the presence of various endogenous factors. Due to the recent advances in cell-expression systems, membrane-protein purification techniques, and labeling approaches, it is now possible to study the structural dynamics of GPCRs at a single-molecule level both in vitro and in live cells. In this review, we discuss state-of-the-art techniques and strategies for expressing, purifying, and labeling GPCRs in the context of single-molecule research. We also highlight four recent studies that demonstrate the applications of single-molecule microscopy in revealing the dynamics of GPCRs. These techniques are also useful as complementary methods to verify the results obtained from other structural biology tools like cryo-electron microscopy and x-ray crystallography.
Collapse
Affiliation(s)
- Eugene Agyemang
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Alyssa N Gonneville
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Sriram Tiruvadi-Krishnan
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Rajan Lamichhane
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996, USA; Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.
| |
Collapse
|
4
|
Zhang H, Tian X, Zhang J, Ai HW. Engineering and Characterization of 3-Aminotyrosine-Derived Red Fluorescent Variants of Circularly Permutated Green Fluorescent Protein. BIOSENSORS 2024; 14:54. [PMID: 38275307 PMCID: PMC10813706 DOI: 10.3390/bios14010054] [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: 12/12/2023] [Revised: 01/08/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Introducing 3-aminotyrosine (aY), a noncanonical amino acid (ncAA), into green fluorescent protein (GFP)-like chromophores shows promise for achieving red-shifted fluorescence. However, inconsistent results, including undesired green fluorescent species, hinder the effectiveness of this approach. In this study, we optimized expression conditions for an aY-derived cpGFP (aY-cpGFP). Key factors like rich culture media and oxygen restriction pre- and post-induction enabled high-yield, high-purity production of the red-shifted protein. We also engineered two variants of aY-cpGFP with enhanced brightness by mutating a few amino acid residues surrounding the chromophore. We further investigated the sensitivity of the aY-derived protein to metal ions, reactive oxygen species (ROS), and reactive nitrogen species (RNS). Incorporating aY into cpGFP had minimal impact on metal ion reactivity but increased the response to RNS. Expanding on these findings, we examined aY-cpGFP expression in mammalian cells and found that reductants in the culture media significantly increased the red-emitting product. Our study indicates that optimizing expression conditions to promote a reduced cellular state proved effective in producing the desired red-emitting product in both E. coli and mammalian cells, while targeted mutagenesis-based protein engineering can further enhance brightness and increase method robustness.
Collapse
Affiliation(s)
- Hao Zhang
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA; (H.Z.); (X.T.); (J.Z.)
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Xiaodong Tian
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA; (H.Z.); (X.T.); (J.Z.)
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jing Zhang
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA; (H.Z.); (X.T.); (J.Z.)
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui-wang Ai
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA; (H.Z.); (X.T.); (J.Z.)
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- The UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
| |
Collapse
|
5
|
Gulyak EL, Alferova VA, Korshun VA, Sapozhnikova KA. Introduction of Carbonyl Groups into Antibodies. Molecules 2023; 28:7890. [PMID: 38067618 PMCID: PMC10707781 DOI: 10.3390/molecules28237890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Antibodies and their derivatives (scFv, Fabs, etc.) represent a unique class of biomolecules that combine selectivity with the ability to target drug delivery. Currently, one of the most promising endeavors in this field is the development of molecular diagnostic tools and antibody-based therapeutic agents, including antibody-drug conjugates (ADCs). To meet this challenge, it is imperative to advance methods for modifying antibodies. A particularly promising strategy involves the introduction of carbonyl groups into the antibody that are amenable to further modification by biorthogonal reactions, namely aliphatic, aromatic, and α-oxo aldehydes, as well as aliphatic and aryl-alkyl ketones. In this review, we summarize the preparation methods and applications of site-specific antibody conjugates that are synthesized using this approach.
Collapse
Affiliation(s)
| | | | | | - Ksenia A. Sapozhnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.L.G.); (V.A.A.); (V.A.K.)
| |
Collapse
|
6
|
Liang M, Yang Y, Zhang J, Sun Y, Peng H, Yi H, Wang Q, Gao X. Use of non-canonical amino acids in genetic code expansion-based therapeutics: Effects on mouse gut microbiota. Microb Biotechnol 2023; 16:2278-2291. [PMID: 37874686 PMCID: PMC10686157 DOI: 10.1111/1751-7915.14358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
Vaccines and cell therapeutics based on genetic code expansion are emerging. A crucial step in these therapeutic technologies is the oral administration of non-canonical amino acids (ncAAs) to control pathogen growth and therapeutic protein levels in vivo. Investigating the toxicity effects of ncAAs can help identify more suitable candidates for developing genetic code expansion-based vaccines and cell therapeutics. In this study, we determined the effects of three ncAAs, namely, 4-acetyl-phenylalanine (pAcF), 4-iodo-phenylalanine (pIoF), and 4-methoxy-phenylalanine (pMeoF), commonly used in genetic code expansion-based vaccines and cell therapeutics, on the main organs, serum biochemical parameters, and gut microbiota in mice. We observed that pIoF and pMeoF significantly altered serum biochemical parameters to some extent. Moreover, the alterations in the mouse gut microbial composition were considerably greater after the oral administration of pIoF and pMeoF than after that of pAcF, compared with that in the control mice. These findings suggest that pAcF is more suitable than pIoF and pMeoF for application in genetic code expansion-based vaccines and cell therapeutics as it disturbs the physiological and gut microecological balance in mice to a lesser extent.
Collapse
Affiliation(s)
- Manyu Liang
- Green Pharmaceutical Technology Key Laboratory of Luzhou, School of PharmacySouthwest Medical UniversityLuzhouChina
| | - Yanhong Yang
- Green Pharmaceutical Technology Key Laboratory of Luzhou, School of PharmacySouthwest Medical UniversityLuzhouChina
| | - Jing Zhang
- Green Pharmaceutical Technology Key Laboratory of Luzhou, School of PharmacySouthwest Medical UniversityLuzhouChina
| | - Yingjie Sun
- Green Pharmaceutical Technology Key Laboratory of Luzhou, School of PharmacySouthwest Medical UniversityLuzhouChina
| | - Haixia Peng
- Green Pharmaceutical Technology Key Laboratory of Luzhou, School of PharmacySouthwest Medical UniversityLuzhouChina
| | - Huawei Yi
- Clinical LaboratoryFirst Affiliated Hospital of Yangtze UniversityJingzhouChina
| | - Qin Wang
- Dazhou Vocational College of Chinese MedicineDazhouChina
| | - Xiaowei Gao
- Green Pharmaceutical Technology Key Laboratory of Luzhou, School of PharmacySouthwest Medical UniversityLuzhouChina
- Dazhou Vocational College of Chinese MedicineDazhouChina
| |
Collapse
|
7
|
van Stevendaal MME, Hazegh Nikroo A, Mason AF, Jansen J, Yewdall NA, van Hest JCM. Regulating Chemokine-Receptor Interactions through the Site-Specific Bioorthogonal Conjugation of Photoresponsive DNA Strands. Bioconjug Chem 2023; 34:2089-2095. [PMID: 37856672 PMCID: PMC10655040 DOI: 10.1021/acs.bioconjchem.3c00390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/30/2023] [Indexed: 10/21/2023]
Abstract
Oligonucleotide conjugation has emerged as a versatile molecular tool for regulating protein activity. A state-of-the-art labeling strategy includes the site-specific conjugation of DNA, by employing bioorthogonal groups genetically incorporated in proteins through unnatural amino acids (UAAs). The incorporation of UAAs in chemokines has to date, however, remained underexplored, probably due to their sometimes poor stability following recombinant expression. In this work, we designed a fluorescent stromal-derived factor-1β (SDF-1β) chemokine fusion protein with a bioorthogonal functionality amenable for click reactions. Using amber stop codon suppression, p-azido-L-phenylalanine was site-specifically incorporated in the fluorescent N-terminal fusion partner, superfolder green fluorescent protein (sfGFP). Conjugation to single-stranded DNAs (ssDNA), modified with a photocleavable spacer and a reactive bicyclononyne moiety, was performed to create a DNA-caged species that blocked the receptor binding ability. This inhibition was completely reversible by means of photocleavage of the ssDNA strands. The results described herein provide a versatile new direction for spatiotemporally regulating chemokine-receptor interactions, which is promising for tissue engineering purposes.
Collapse
Affiliation(s)
- Marleen
H. M. E. van Stevendaal
- Laboratory
of Bio-Organic Chemistry, Department of Biomedical Engineering, Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Arjan Hazegh Nikroo
- Laboratory
of Bio-Organic Chemistry, Department of Biomedical Engineering, Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Alexander F. Mason
- School
of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jitske Jansen
- Department
of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - N. Amy Yewdall
- School
of Biological Sciences, University of Canterbury, 8041 Christchurch, New Zealand
| | - Jan C. M. van Hest
- Laboratory
of Bio-Organic Chemistry, Department of Biomedical Engineering, Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| |
Collapse
|
8
|
Ponzar N, Pozzi N. Probing the conformational dynamics of thiol-isomerases using non-canonical amino acids and single-molecule FRET. Methods 2023; 214:8-17. [PMID: 37068599 PMCID: PMC10203983 DOI: 10.1016/j.ymeth.2023.04.004] [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: 03/10/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023] Open
Abstract
Disulfide bonds drive protein correct folding, prevent protein aggregation, and stabilize three-dimensional structures of proteins and their assemblies. Dysregulation of this activity leads to several disorders, including cancer, neurodegeneration, and thrombosis. A family of 20+ enzymes, called thiol-isomerases (TIs), oversee this process in the endoplasmic reticulum of human cells to ensure efficacy and accuracy. While the biophysical and biochemical properties of cysteine residues are well-defined, our structural knowledge of how TIs select, interact and process their substrates remains poorly understood. How TIs structurally and functionally respond to changes in redox environment and other post-translational modifications remain unclear, too. We recently developed a workflow for site-specific incorporation of non-canonical amino acids into protein disulfide isomerase (PDI), the prototypical member of TIs. Combined with click chemistry, this strategy enabled us to perform single-molecule biophysical studies of PDI under various solution conditions. This paper details protocols and discusses challenges in performing these experiments. We expect this approach, combined with other emerging technologies in single-molecule biophysics and structural biology, to facilitate the exploration of the mechanisms by which TIs carry out their fascinating but poorly understood roles in humans, especially in the context of thrombosis.
Collapse
Affiliation(s)
- Nathan Ponzar
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
| |
Collapse
|
9
|
Ebrahimi SB, Samanta D. Engineering protein-based therapeutics through structural and chemical design. Nat Commun 2023; 14:2411. [PMID: 37105998 PMCID: PMC10132957 DOI: 10.1038/s41467-023-38039-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Protein-based therapeutics have led to new paradigms in disease treatment. Projected to be half of the top ten selling drugs in 2023, proteins have emerged as rivaling and, in some cases, superior alternatives to historically used small molecule-based medicines. This review chronicles both well-established and emerging design strategies that have enabled this paradigm shift by transforming protein-based structures that are often prone to denaturation, degradation, and aggregation in vitro and in vivo into highly effective therapeutics. In particular, we discuss strategies for creating structures with increased affinity and targetability, enhanced in vivo stability and pharmacokinetics, improved cell permeability, and reduced amounts of undesired immunogenicity.
Collapse
Affiliation(s)
- Sasha B Ebrahimi
- Drug Product Development-Steriles, GlaxoSmithKline, Collegeville, PA, 19426, USA.
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA.
| |
Collapse
|
10
|
Case M, Navaratna T, Vinh J, Thurber G. Rapid Evaluation of Staple Placement in Stabilized α Helices Using Bacterial Surface Display. ACS Chem Biol 2023; 18:905-914. [PMID: 37039514 PMCID: PMC10773984 DOI: 10.1021/acschembio.3c00048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
There are a wealth of proteins involved in disease that cannot be targeted by current therapeutics because they are inside cells, inaccessible to most macromolecules, and lack small-molecule binding pockets. Stapled peptides, where two amino acids are covalently linked, form a class of macrocycles that have the potential to penetrate cell membranes and disrupt intracellular protein-protein interactions. However, their discovery relies on solid-phase synthesis, greatly limiting queries into their complex design space involving amino acid sequence, staple location, and staple chemistry. Here, we use stabilized peptide engineering by Escherichia coli display (SPEED), which utilizes noncanonical amino acids and click chemistry for stabilization, to rapidly screen staple location and linker structure to accelerate peptide design. After using SPEED to confirm hotspots in the mdm2-p53 interaction, we evaluated different staple locations and staple chemistry to identify several novel nanomolar and sub-nanomolar antagonists. Next, we evaluated SPEED in the B cell lymphoma 2 (Bcl-2) protein family, which is responsible for regulating apoptosis. We report that novel staple locations modified in the context of BIM, a high affinity but nonspecific naturally occurring peptide, improve its specificity against the highly homologous proteins in the Bcl-2 family. These compounds demonstrate the importance of screening linker location and chemistry in identifying high affinity and specific peptide antagonists. Therefore, SPEED can be used as a versatile platform to evaluate multiple design criteria for stabilized peptide engineering.
Collapse
|
11
|
Beyond luciferase-luciferin system: Modification, improved imaging and biomedical application. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
12
|
Salar S, Schubot FD. Biochemical analysis of protein-protein interfaces underlying the regulation of bacterial secretion systems. Methods Enzymol 2022; 679:1-32. [PMID: 36682859 DOI: 10.1016/bs.mie.2022.07.030] [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] [Indexed: 12/12/2022]
Abstract
Bacterial pathogens such as Pseudomonas aeruginosa use complex regulatory networks to tailor gene expression patterns to meet complex environmental challenges. P. aeruginosa is capable of causing both acute and chronic persistent infections, each type being characterized by distinct symptoms brought about by distinct sets of virulence mechanisms. The GacS/GacA phosphorelay system sits at the heart of a complex regulatory network that reciprocally governs the expression of virulence factors associated with either acute or chronic infections. A second non-enzymatic signaling cascade involving four proteins, ExsA, ExsC, ExsD, and ExsE is a key player in regulating the expression of the type three secretion system, an essential facilitator of acute infections. Both signaling pathways involve a remarkable array of non-canonical interactions that we sought to characterize. In the following section, we will outline several strategies, we adapted to map protein-protein interfaces and quantify the strength of biomolecular interactions by pairing complex mutational analyses with FRET binding assays and Bacterial-Two-Hybrid assays with appropriate functional assays. In the process, protocols were developed for disrupting large hydrophobic interfaces, deleting entire domains within a protein, and for mapping protein-protein interfaces formed primarily through backbone interactions.
Collapse
Affiliation(s)
- Safoura Salar
- Department of Biological Sciences, Virginia Polytechnic Institute & State University, Blacksburg, VA, United States
| | - Florian D Schubot
- Department of Biological Sciences, Virginia Polytechnic Institute & State University, Blacksburg, VA, United States.
| |
Collapse
|
13
|
Striving for sustainable biosynthesis: discovery, diversification, and production of antimicrobial drugs in Escherichia coli. Biochem Soc Trans 2022; 50:1315-1328. [PMID: 36196987 DOI: 10.1042/bst20220218] [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: 07/14/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022]
Abstract
New antimicrobials need to be discovered to fight the advance of multidrug-resistant pathogens. A promising approach is the screening for antimicrobial agents naturally produced by living organisms. As an alternative to studying the native producer, it is possible to use genetically tractable microbes as heterologous hosts to aid the discovery process, facilitate product diversification through genetic engineering, and ultimately enable environmentally friendly production. In this mini-review, we summarize the literature from 2017 to 2022 on the application of Escherichia coli and E. coli-based platforms as versatile and powerful systems for the discovery, characterization, and sustainable production of antimicrobials. We highlight recent developments in high-throughput screening methods and genetic engineering approaches that build on the strengths of E. coli as an expression host and that led to the production of antimicrobial compounds. In the last section, we briefly discuss new techniques that have not been applied to discover or engineer antimicrobials yet, but that may be useful for this application in the future.
Collapse
|
14
|
Meganathan I, Sundarapandian A, Shanmugam G, Ayyadurai N. Three-dimensional tailor-made collagen-like proteins hydrogel for tissue engineering applications. BIOMATERIALS ADVANCES 2022; 139:212997. [PMID: 35882145 DOI: 10.1016/j.bioadv.2022.212997] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/23/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Despite the potential tunable properties of blank slate collagen-like proteins (CLP), an alternative to animal-originated collagen, assembling them into a stable 3D hydrogel to mimic extracellular matrix is a challenge. To address this constraint, the CLP (without hydroxyproline, CLPpro) and its variants encoding functional unnatural amino acids such as hydroxyproline (CLPhyp) and 3,4-dihydroxyphenylalanine (CLPdopa) were generated through genetic code engineering for 3D hydrogel development. The CLPhyp and CLPdopa were chosen to enhance the intermolecular hydrogen bond interaction through additional hydroxyl moiety and thereby facilitate the self-assembly into a fibrillar network of the hydrogel. Hydrogelation was induced through genipin as a cross-linker, enabling intermolecular cross-linking to form a hydrogel. Spectroscopic and rheological analyses confirmed that CLPpro and its variants maintained native triple-helical structure, which is necessary for its function, and viscoelastic nature of the hydrogels, respectively. Unlike CLPpro, the varients (CLPhyp and CLPdopa) increased pore size formation in the hydrogel scaffold, facilitating 3T3 fibroblast cell interactions. DSC analysis indicated that the stability of the hydrogels got increased upon the genetic incorporation of hydroxyproline (CLPhyp) and dopa (CLPdopa) in CLPpro. In addition, CLPdopa hydrogel was found to be relatively stable against collagenase enzyme compared to CLPpro and CLPhyp. It is the first report on 3D biocompatible hydrogel preparation by tailoring CLP sequence with non-natural amino acids. These next-generation tunable CLP hydrogels open a new venue to design synthetic protein-based biocompatible 3D biomaterials for tissue engineering applications.
Collapse
Affiliation(s)
- Ilamaran Meganathan
- Division of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute, Chennai, Tamilnadu, India
| | - Ashokraj Sundarapandian
- Division of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute, Chennai, Tamilnadu, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Ganesh Shanmugam
- Division of Organic and Bioorganic Chemistry, Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute, Chennai, Tamilnadu, India.
| | - Niraikulam Ayyadurai
- Division of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute, Chennai, Tamilnadu, India.
| |
Collapse
|
15
|
Stieglitz JT, Van Deventer JA. High-Throughput Aminoacyl-tRNA Synthetase Engineering for Genetic Code Expansion in Yeast. ACS Synth Biol 2022; 11:2284-2299. [PMID: 35793554 PMCID: PMC10065163 DOI: 10.1021/acssynbio.1c00626] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein expression with genetically encoded noncanonical amino acids (ncAAs) benefits a broad range of applications, from the discovery of biological therapeutics to fundamental biological studies. A major factor limiting the use of ncAAs is the lack of orthogonal translation systems (OTSs) that support efficient genetic code expansion at repurposed stop codons. Aminoacyl-tRNA synthetases (aaRSs) have been extensively evolved in Escherichia coli but are not always orthogonal in eukaryotes. In this work, we use a yeast display-based ncAA incorporation reporter platform with fluorescence-activated cell sorting to screen libraries of aaRSs in high throughput for (1) the incorporation of ncAAs not previously encoded in yeast; (2) the improvement of the performance of an existing aaRS; (3) highly selective OTSs capable of discriminating between closely related ncAA analogues; and (4) OTSs exhibiting enhanced polyspecificity to support translation with structurally diverse sets of ncAAs. The number of previously undiscovered aaRS variants we report in this work more than doubles the total number of translationally active aaRSs available for genetic code manipulation in yeast. The success of myriad screening strategies has important implications related to the fundamental properties and evolvability of aaRSs. Furthermore, access to OTSs with diverse activities and specific or polyspecific properties is invaluable for a range of applications within chemical biology, synthetic biology, and protein engineering.
Collapse
Affiliation(s)
- Jessica T Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - James A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| |
Collapse
|
16
|
Kaur R, Banga S, Babu SA. Construction of carbazole-based unnatural amino acid scaffolds via Pd(II)-catalyzed C(sp 3)-H functionalization. Org Biomol Chem 2022; 20:4391-4414. [PMID: 35583129 DOI: 10.1039/d2ob00658h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report the synthesis of carbazole-based unnatural α-amino acid and non-α-amino acid derivatives via a Pd(II)-catalyzed bidentate directing group 8-aminoquinoline-aided β-C(sp3)-H activation/functionalization method. Various N-phthaloyl, DL-, L- and D-carboxamides derived from their corresponding α-amino acids, non-α-amino acids and aliphatic carboxamides were subjected to the β-C(sp3)-H functionalization with 3-iodocarbazoles in the presence of a Pd(II) catalyst to afford the corresponding carbazole moiety installed unnatural amino acid derivatives and aliphatic carboxamides. Carbazole motif-containing racemic (DL) and enantiopure (L and D) amino acid derivatives including phenylalanine, norvaline, leucine, norleucine and 2-aminooctanoic acid with anti-stereochemistry and various non-α-amino acid derivatives including GABA have been synthesized. Removal of the 8-aminoquinoline directing group, deprotection of the phthalimide moiety and the preparation of carbazole amino acid derivatives containing free amino- and carboxylate groups are shown. The carbazole motif is prevalent in alkaloids and biologically active molecules and functional materials. Thus, this work on the synthesis of carbazole-based unnatural amino acid derivatives would enrich the libraries of unnatural amino acid derivatives and carbazoles.
Collapse
Affiliation(s)
- Ramandeep Kaur
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306, India.
| | - Shefali Banga
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306, India.
| | - Srinivasarao Arulananda Babu
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306, India.
| |
Collapse
|
17
|
Del Bino L, Østerlid KE, Wu DY, Nonne F, Romano MR, Codée J, Adamo R. Synthetic Glycans to Improve Current Glycoconjugate Vaccines and Fight Antimicrobial Resistance. Chem Rev 2022; 122:15672-15716. [PMID: 35608633 PMCID: PMC9614730 DOI: 10.1021/acs.chemrev.2c00021] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Antimicrobial resistance (AMR) is emerging as the next potential pandemic. Different microorganisms, including the bacteria Acinetobacter baumannii, Clostridioides difficile, Escherichia coli, Enterococcus faecium, Klebsiella pneumoniae, Neisseria gonorrhoeae, Pseudomonas aeruginosa, non-typhoidal Salmonella, and Staphylococcus aureus, and the fungus Candida auris, have been identified by the WHO and CDC as urgent or serious AMR threats. Others, such as group A and B Streptococci, are classified as concerning threats. Glycoconjugate vaccines have been demonstrated to be an efficacious and cost-effective measure to combat infections against Haemophilus influenzae, Neisseria meningitis, Streptococcus pneumoniae, and, more recently, Salmonella typhi. Recent times have seen enormous progress in methodologies for the assembly of complex glycans and glycoconjugates, with developments in synthetic, chemoenzymatic, and glycoengineering methodologies. This review analyzes the advancement of glycoconjugate vaccines based on synthetic carbohydrates to improve existing vaccines and identify novel candidates to combat AMR. Through this literature survey we built an overview of structure-immunogenicity relationships from available data and identify gaps and areas for further research to better exploit the peculiar role of carbohydrates as vaccine targets and create the next generation of synthetic carbohydrate-based vaccines.
Collapse
Affiliation(s)
| | - Kitt Emilie Østerlid
- Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, The Netherlands
| | - Dung-Yeh Wu
- Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, The Netherlands
| | | | | | - Jeroen Codée
- Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, The Netherlands
| | | |
Collapse
|
18
|
Cory MB, Hostetler ZM, Kohli RM. Kinetic dissection of macromolecular complex formation with minimally perturbing fluorescent probes. Methods Enzymol 2022; 664:151-171. [PMID: 35331372 DOI: 10.1016/bs.mie.2022.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The formation of macromolecular complexes containing multiple protein binding partners is at the core of many biochemical pathways. Studying the kinetics of complex formation can offer significant biological insights and complement static structural snapshots or approaches that reveal thermodynamic affinities. However, determining the kinetics of macromolecular complex formation can be difficult without significant manipulations to the system. Fluorescence anisotropy using a fluorophore-labeled constituent of the biologic complex offers potential advantages in obtaining time-resolved signals tracking complex assembly. However, an inherent challenge of traditional post-translational protein labeling is the orthogonality of labeling chemistry with regards to protein target and the potential disruption of complex formation. In this chapter, we will discuss the application of unnatural amino acid labeling as a means for generating a minimally perturbing reporter. We then describe the use of fluorescence anisotropy to define the kinetics of complex formation, using the key protein-protein-nucleic acid complex governing the bacterial DNA damage response-RecA nucleoprotein filaments binding to LexA-as a model system. We will also show how this assay can be expanded to ask questions about the kinetics of complex formation for unlabeled variants, thus assessing assembly kinetics in more native contexts and broadening its utility. We discuss the optimization process for our model system and offer guidelines for applying the same principles to other macromolecular systems.
Collapse
Affiliation(s)
- Michael B Cory
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Zachary M Hostetler
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| |
Collapse
|
19
|
Guan I, Williams K, Liu JST, Liu X. Synthetic Thiol and Selenol Derived Amino Acids for Expanding the Scope of Chemical Protein Synthesis. Front Chem 2022; 9:826764. [PMID: 35237567 PMCID: PMC8883728 DOI: 10.3389/fchem.2021.826764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/29/2021] [Indexed: 01/18/2023] Open
Abstract
Cells employ post-translational modifications (PTMs) as key mechanisms to expand proteome diversity beyond the inherent limitations of a concise genome. The ability to incorporate post-translationally modified amino acids into protein targets via chemical ligation of peptide fragments has enabled the access to homogeneous proteins bearing discrete PTM patterns and empowered functional elucidation of individual modification sites. Native chemical ligation (NCL) represents a powerful and robust means for convergent assembly of two homogeneous, unprotected peptides bearing an N-terminal cysteine residue and a C-terminal thioester, respectively. The subsequent discovery that protein cysteine residues can be chemoselectively desulfurized to alanine has ignited tremendous interest in preparing unnatural thiol-derived variants of proteogenic amino acids for chemical protein synthesis following the ligation-desulfurization logic. Recently, the 21st amino acid selenocysteine, together with other selenyl derivatives of amino acids, have been shown to facilitate ultrafast ligation with peptidyl selenoesters, while the advancement in deselenization chemistry has provided reliable bio-orthogonality to PTMs and other amino acids. The combination of these ligation techniques and desulfurization/deselenization chemistries has led to streamlined synthesis of multiple structurally-complex, post-translationally modified proteins. In this review, we aim to summarize the latest chemical synthesis of thiolated and selenylated amino-acid building blocks and exemplify their important roles in conquering challenging protein targets with distinct PTM patterns.
Collapse
Affiliation(s)
- Ivy Guan
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
- The Heart Research Institute, The University of Sydney, Sydney, NSW, Australia
| | - Kayla Williams
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
- The Heart Research Institute, The University of Sydney, Sydney, NSW, Australia
| | - Joanna Shu Ting Liu
- The Heart Research Institute, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Xuyu Liu
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
- The Heart Research Institute, The University of Sydney, Sydney, NSW, Australia
- *Correspondence: Xuyu Liu,
| |
Collapse
|
20
|
Obeng EM, Dzuvor CKO, Danquah MK. Anti-SARS-CoV-1 and -2 nanobody engineering towards avidity-inspired therapeutics. NANO TODAY 2022; 42:101350. [PMID: 34840592 PMCID: PMC8608585 DOI: 10.1016/j.nantod.2021.101350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/22/2021] [Accepted: 11/18/2021] [Indexed: 05/15/2023]
Abstract
In the past two decades, the emergence of coronavirus diseases has been dire distress on both continental and global fronts and has resulted in the search for potent treatment strategies. One crucial challenge in this search is the recurrent mutations in the causative virus spike protein, which lead to viral escape issues. Among the current promising therapeutic discoveries is the use of nanobodies and nanobody-like molecules. While these nanobodies have demonstrated high-affinity interaction with the virus, the unpredictable spike mutations have warranted the need for avidity-inspired therapeutics of potent inhibitors such as nanobodies. This article discusses novel approaches for the design of anti-SARS-CoV-1 and -2 nanobodies to facilitate advanced innovations in treatment technologies. It further discusses molecular interactions and suggests multivalent protein nanotechnology and chemistry approaches to translate mere molecular affinity into avidity.
Collapse
Affiliation(s)
- Eugene M Obeng
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Bioengineering Laboratory, Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Christian K O Dzuvor
- Bioengineering Laboratory, Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, United States
| |
Collapse
|
21
|
Lee BS, Choi WJ, Lee SW, Ko BJ, Yoo TH. Towards Engineering an Orthogonal Protein Translation Initiation System. Front Chem 2021; 9:772648. [PMID: 34765589 PMCID: PMC8576571 DOI: 10.3389/fchem.2021.772648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/14/2021] [Indexed: 11/24/2022] Open
Abstract
In the last two decades, methods to incorporate non-canonical amino acids (ncAAs) into specific positions of a protein have advanced significantly; these methods have become general tools for engineering proteins. However, almost all these methods depend on the translation elongation process, and strategies leveraging the initiation process have rarely been reported. The incorporation of a ncAA specifically at the translation initiation site enables the installation of reactive groups for modification at the N-termini of proteins, which are attractive positions for introducing abiological groups with minimal structural perturbations. In this study, we attempted to engineer an orthogonal protein translation initiation system. Introduction of the identity elements of Escherichia coli initiator tRNA converted an engineered Methanococcus jannaschii tRNATyr into an initiator tRNA. The engineered tRNA enabled the site-specific incorporation of O-propargyl-l-tyrosine (OpgY) into the amber (TAG) codon at the translation initiation position but was inactive toward the elongational TAG codon. Misincorporation of Gln was detected, and the engineered system was demonstrated only with OpgY. We expect further engineering of the initiator tRNA for improved activity and specificity to generate an orthogonal translation initiation system.
Collapse
Affiliation(s)
- Byeong Sung Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Woon Jong Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sang Woo Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Byoung Joon Ko
- School of Biopharmaceutical and Medical Sciences, Sungshin Women's University, Seoul, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
| |
Collapse
|
22
|
Graf LG, Vogt R, Blasl AT, Qin C, Schulze S, Zühlke D, Sievers S, Lammers M. Assays to Study Enzymatic and Non-Enzymatic Protein Lysine Acetylation In Vitro. Curr Protoc 2021; 1:e277. [PMID: 34748287 DOI: 10.1002/cpz1.277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Proteins can be lysine-acetylated both enzymatically, by lysine acetyltransferases (KATs), and non-enzymatically, by acetyl-CoA and/or acetyl-phosphate. Such modification can be reversed by lysine deacetylases classified as NAD+ -dependent sirtuins or by classical Zn2+ -dependent deacetylases (KDACs). The regulation of protein lysine acetylation events by KATs and sirtuins/KDACs, or by non-enzymatic processes, is often assessed only indirectly by mass spectrometry or by mutational studies in cells. Mutational approaches to study lysine acetylation are limited, as these often poorly mimic lysine acetylation. Here, we describe protocols to assess the direct regulation of protein lysine acetylation by both sirtuins/KDACs and KATs, as well as non-enzymatically. We first describe a protocol for the production of site-specific lysine-acetylated proteins using a synthetic biological approach, the genetic code expansion concept (GCEC). These natively folded, lysine-acetylated proteins can then be used as direct substrates for sirtuins and KDACs. This approach addresses various limitations encountered with other methods. First, results from sirtuin/KDAC-catalyzed deacetylation assays obtained using acetylated peptides as substrates can vary considerably compared to experiments using natively folded substrate proteins. In addition, producing lysine-acetylated proteins for deacetylation assays by using recombinantly expressed KATs is difficult, as these often do not yield proteins that are homogeneously and quantitatively lysine acetylated. Moreover, KATs are often huge multi-domain proteins, which are difficult to recombinantly express and purify in soluble form. We also describe protocols to study the direct regulation of protein lysine acetylation, both enzymatically, by sirtuins/KDACs and KATs, and non-enzymatically, by acetyl-CoA and/or acetyl-phosphate. The latter protocol also includes a section that explains how specific lysine acetylation sites can be detected by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). The protocols described here can be useful for providing a more detailed understanding of the enzymatic and non-enzymatic regulation of lysine acetylation sites, an important aspect to judge their physiological significance. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of N-(ε)-lysine-acetylated proteins using the genetic code expansion concept (GCEC) Basic Protocol 2: In vitro sirtuin (SIRT)-catalyzed deacetylation of lysine-acetylated proteins prepared by the GCEC Basic Protocol 3: In vitro KDAC/HDAC-catalyzed deacetylation of lysine-acetylated proteins Basic Protocol 4: In vitro lysine acetylation of recombinantly expressed proteins by lysine acetyltransferases (KATs) Basic Protocol 5: In vitro non-enzymatic lysine acetylation of proteins by acetyl-CoA and/or acetyl-phosphate.
Collapse
Affiliation(s)
- Leonie G Graf
- Department Synthetic and Structural Biochemistry, University of Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Robert Vogt
- Department Synthetic and Structural Biochemistry, University of Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Anna-Theresa Blasl
- Department Synthetic and Structural Biochemistry, University of Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Chuan Qin
- Department Synthetic and Structural Biochemistry, University of Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Sabrina Schulze
- Department Synthetic and Structural Biochemistry, University of Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Daniela Zühlke
- Department of Microbial Physiology and Molecular Biology, University of Greifswald, Institute of Microbiology, Greifswald, Germany
| | - Susanne Sievers
- Department of Microbial Physiology and Molecular Biology, University of Greifswald, Institute of Microbiology, Greifswald, Germany
| | - Michael Lammers
- Department Synthetic and Structural Biochemistry, University of Greifswald, Institute for Biochemistry, Greifswald, Germany
| |
Collapse
|
23
|
Zhu HQ, Tang XL, Zheng RC, Zheng YG. Recent advancements in enzyme engineering via site-specific incorporation of unnatural amino acids. World J Microbiol Biotechnol 2021; 37:213. [PMID: 34741210 DOI: 10.1007/s11274-021-03177-1] [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: 08/28/2021] [Accepted: 10/23/2021] [Indexed: 11/28/2022]
Abstract
With increased attention to excellent biocatalysts, evolving methods based on nature or unnatural amino acid (UAAs) mutagenesis have become an important part of enzyme engineering. The emergence of powerful method through expanding the genetic code allows to incorporate UAAs with unique chemical functionalities into proteins, endowing proteins with more structural and functional features. To date, over 200 diverse UAAs have been incorporated site-specifically into proteins via this methodology and many of them have been widely exploited in the field of enzyme engineering, making this genetic code expansion approach possible to be a promising tool for modulating the properties of enzymes. In this context, we focus on how this robust method to specifically incorporate UAAs into proteins and summarize their applications in enzyme engineering for tuning and expanding the functional properties of enzymes. Meanwhile, we aim to discuss how the benefits can be achieved by using the genetically encoded UAAs. We hope that this method will become an integral part of the field of enzyme engineering in the future.
Collapse
Affiliation(s)
- Hang-Qin Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Xiao-Ling Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Ren-Chao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China. .,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| |
Collapse
|
24
|
Kim E, Jeon J, Zhu Y, Hoppe ED, Jun YS, Genin GM, Zhang F. A Biosynthetic Hybrid Spidroin-Amyloid-Mussel Foot Protein for Underwater Adhesion on Diverse Surfaces. ACS APPLIED MATERIALS & INTERFACES 2021; 13:48457-48468. [PMID: 34633172 PMCID: PMC10041942 DOI: 10.1021/acsami.1c14182] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Strong underwater adhesives are attractive materials for biomedical healing and underwater repair, but their success in applications has been limited, owing to challenges with underwater setting and with balancing surface adhesion and cohesion. Here, we applied synthetic biology approaches to overcome these challenges through design and synthesis of a novel hybrid protein consisting of the zipper-forming domains of an amyloid protein, flexible spider silk sequences, and a dihydroxyphenylalanine (DOPA)-containing mussel foot protein (Mfp). This partially structured, hybrid protein can self-assemble into a semi-crystalline hydrogel that exhibits high strength and toughness as well as strong underwater adhesion to a variety of surfaces, including difficult-to-adhere plastics, tendon, and skin. The hydrogel allows selective debonding by oxidation or iron-chelating treatments. Both the material design and the biosynthetic approach explored in this study will inspire future work for a wide range of hybrid protein-based materials with tunable properties and broad applications.
Collapse
Affiliation(s)
- Eugene Kim
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
| | - Juya Jeon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
| | - Yaguang Zhu
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
| | - Ethan D. Hoppe
- NSF Science and Technology Center for Engineering MechanoBiology, Department of Mechanical Engineering & Materials Science, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
| | - Young-Shin Jun
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
- Institute of Materials Science and Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
| | - Guy M. Genin
- NSF Science and Technology Center for Engineering MechanoBiology, Department of Mechanical Engineering & Materials Science, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
- Institute of Materials Science and Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
| | - Fuzhong Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
- Institute of Materials Science and Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, Missouri 63130
| |
Collapse
|
25
|
Yi H, Zhang J, Ke F, Guo X, Yang J, Xie P, Liu L, Wang Q, Gao X. Comparative Analyses of the Transcriptome and Proteome of Escherichia coli C321.△A and Further Improving Its Noncanonical Amino Acids Containing Protein Expression Ability by Integration of T7 RNA Polymerase. Front Microbiol 2021; 12:744284. [PMID: 34659179 PMCID: PMC8511705 DOI: 10.3389/fmicb.2021.744284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/30/2021] [Indexed: 01/09/2023] Open
Abstract
Incorporation of noncanonical amino acids (ncAAs) into proteins has been proven to be a powerful tool to manipulate protein structure and function, and to investigate many biological processes. Improving the yields of ncAA-containing proteins is of great significance in industrial-scale applications. Escherichia coli C321.ΔA was generated by the replacement of all known amber codons and the deletion of RF1 in the genome and has been proven to be an ideal host for ncAA-containing protein expression using genetic code expansion. In this study, we investigated the transcriptome and proteome profiles of this first codon reassignment strain and found that some functions and metabolic pathways were differentially expressed when compared with those of its parent strain. Genes involved in carbohydrate and energy metabolism were remarkably downregulated. Our results may provide important clues about the growth defects in E. coli C321.ΔA. Furthermore, we improved the yields of ncAA-containing proteins in E. coli C321.ΔA by integrating the T7 RNA polymerase system.
Collapse
Affiliation(s)
- Huawei Yi
- Clinical Laboratory, The First Affiliated Hospital of Yangtze University, Jingzhou, China
| | - Jing Zhang
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Famin Ke
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xiurong Guo
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jian Yang
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Peijuan Xie
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Li Liu
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Qin Wang
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xiaowei Gao
- School of Pharmacy, Southwest Medical University, Luzhou, China.,Department of Chemistry, Zhejiang University, Hangzhou, China
| |
Collapse
|
26
|
Living fabrication of functional semi-interpenetrating polymeric materials. Nat Commun 2021; 12:3422. [PMID: 34103521 PMCID: PMC8187375 DOI: 10.1038/s41467-021-23812-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 05/11/2021] [Indexed: 01/02/2023] Open
Abstract
Cell-mediated living fabrication has great promise for generating materials with versatile, programmable functions. Here, we demonstrate the engineering of living materials consisting of semi-interpenetrating polymer networks (sIPN). The fabrication process is driven by the engineered bacteria encapsulated in a polymeric microcapsule, which serves as the initial scaffold. The bacteria grow and undergo programmed lysis in a density-dependent manner, releasing protein monomers decorated with reactive tags. Those protein monomers polymerize with each other to form the second polymeric component that is interlaced with the initial crosslinked polymeric scaffold. The formation of sIPN serves the dual purposes of enhancing the mechanical property of the living materials and anchoring effector proteins for diverse applications. The material is resilient to perturbations because of the continual assembly of the protein mesh from the monomers released by the engineered bacteria. We demonstrate the adoption of the platform to protect gut microbiota in animals from antibiotic-mediated perturbations. Our work lays the foundation for programming functional living materials for diverse applications.
Collapse
|
27
|
Kofman C, Lee J, Jewett MC. Engineering molecular translation systems. Cell Syst 2021; 12:593-607. [PMID: 34139167 DOI: 10.1016/j.cels.2021.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/19/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022]
Abstract
Molecular translation systems provide a genetically encoded framework for protein synthesis, which is essential for all life. Engineering these systems to incorporate non-canonical amino acids (ncAAs) into peptides and proteins has opened many exciting opportunities in chemical and synthetic biology. Here, we review recent advances that are transforming our ability to engineer molecular translation systems. In cell-based systems, new processes to synthesize recoded genomes, tether ribosomal subunits, and engineer orthogonality with high-throughput workflows have emerged. In cell-free systems, adoption of flexizyme technology and cell-free ribosome synthesis and evolution platforms are expanding the limits of chemistry at the ribosome's RNA-based active site. Looking forward, innovations will deepen understanding of molecular translation and provide a path to polymers with previously unimaginable structures and functions.
Collapse
Affiliation(s)
- Camila Kofman
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joongoo Lee
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Department of Chemical Engineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Interdisplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA; Simpson Querrey Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| |
Collapse
|
28
|
Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
Collapse
Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| |
Collapse
|
29
|
Wątły J, Miller A, Kozłowski H, Rowińska-Żyrek M. Peptidomimetics - An infinite reservoir of metal binding motifs in metabolically stable and biologically active molecules. J Inorg Biochem 2021; 217:111386. [PMID: 33610030 DOI: 10.1016/j.jinorgbio.2021.111386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022]
Abstract
The involvement of metal ions in interactions with therapeutic peptides is inevitable. They are one of the factors able to fine-tune the biological properties of antimicrobial peptides, a promising group of drugs with one large drawback - a problematic metabolic stability. Appropriately chosen, proteolytically stable peptidomimetics seem to be a reasonable solution of the problem, and the use of D-, β-, γ-amino acids, unnatural amino acids, azapeptides, peptoids, cyclopeptides and dehydropeptides is an infinite reservoir of metal binding motifs in metabolically stable, well-designed, biologically active molecules. Below, their specific structural features, metal-chelating abilities and antimicrobial potential are discussed.
Collapse
Affiliation(s)
- Joanna Wątły
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland.
| | - Adriana Miller
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland
| | - Henryk Kozłowski
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland; Department of Health Sciences, University of Opole, Katowicka 68, Opole 45-060, Poland
| | | |
Collapse
|
30
|
Yoshida Y, Kasuya R, Mino T, Sakamoto M. Phase-transfer catalysed asymmetric synthesis of α-chiral tetrasubstituted α-aminothioesters. Org Biomol Chem 2021; 19:6402-6406. [PMID: 34100506 DOI: 10.1039/d1ob00829c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chiral amino thioesters are important scaffolds owing to their widespread use in organic synthesis and biosynthesis. Despite their usefulness, their asymmetric synthesis, especially the catalytic asymmetric synthesis of α-chiral tetrasubstituted α-aminothioesters, is limited, with only one example reported so far. Herein, we report the first phase-transfer catalysed asymmetric synthesis of α-chiral tetrasubstituted α-aminothioesters to afford the corresponding products in up to 81% ee.
Collapse
Affiliation(s)
- Yasushi Yoshida
- Molecular Chirality Research Center, Graduate School of Engineering, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba-shi, Chiba 263-8522, Japan.
| | - Reina Kasuya
- Molecular Chirality Research Center, Graduate School of Engineering, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba-shi, Chiba 263-8522, Japan.
| | - Takashi Mino
- Molecular Chirality Research Center, Graduate School of Engineering, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba-shi, Chiba 263-8522, Japan.
| | - Masami Sakamoto
- Molecular Chirality Research Center, Graduate School of Engineering, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba-shi, Chiba 263-8522, Japan.
| |
Collapse
|
31
|
Park J, Lee S, Kim Y, Yoo TH. Methods to generate site-specific conjugates of antibody and protein. Bioorg Med Chem 2021; 30:115946. [DOI: 10.1016/j.bmc.2020.115946] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023]
|
32
|
Grigoletto A, Tedeschini T, Canato E, Pasut G. The evolution of polymer conjugation and drug targeting for the delivery of proteins and bioactive molecules. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 13:e1689. [PMID: 33314717 DOI: 10.1002/wnan.1689] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/11/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022]
Abstract
Polymer conjugation can be considered one of the leading approaches within the vast field of nanotechnology-based drug delivery systems. In fact, such technology can be exploited for delivering an active molecule, such as a small drug, a protein, or genetic material, or it can be applied to other drug delivery systems as a strategy to improve their in vivo behavior or pharmacokinetic activities such as prolonging the half-life of a drug, conferring stealth properties, providing external stimuli responsiveness, and so on. If on the one hand, polymer conjugation with biotech drug is considered the linchpin of the protein delivery field boasting several products in clinical use, on the other, despite dedicated research, conjugation with low molecular weight drugs has not yet achieved the milestone of the first clinical approval. Some of the primary reasons for this debacle are the difficulties connected to achieving selective targeting to diseased tissue, organs, or cells, which is the main goal not only of polymer conjugation but of all delivery systems of small drugs. In light of the need to achieve better drug targeting, researchers are striving to identify more sophisticated, biocompatible delivery approaches and to open new horizons for drug targeting methodologies leading to successful clinical applications. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Toxicology and Regulatory Issues in Nanomedicine > Regulatory and Policy Issues in Nanomedicine.
Collapse
Affiliation(s)
- Antonella Grigoletto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Tommaso Tedeschini
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Elena Canato
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Gianfranco Pasut
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| |
Collapse
|
33
|
Liu M, Thijssen V, Jongkees SAK. Suppression of Formylation Provides an Alternative Approach to Vacant Codon Creation in Bacterial In Vitro Translation. Angew Chem Int Ed Engl 2020; 59:21870-21874. [PMID: 32840944 PMCID: PMC7756408 DOI: 10.1002/anie.202003779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/04/2020] [Indexed: 11/22/2022]
Abstract
Genetic code reprogramming is a powerful approach to controlled protein modification. A remaining challenge, however, is the generation of vacant codons. We targeted the initiation machinery of E. coli, showing that restriction of the formyl donor or inhibition of the formyl transferase during in vitro translation is sufficient to prevent formylation of the acylated initiating tRNA and thereby create a vacant initiation codon that can be reprogrammed by exogenously charged tRNA. Our approach conveniently generates peptides and proteins tagged N‐terminally with non‐canonical functional groups at up to 99 % reprogramming efficiency, in combination with decoding the AUG elongation codons either with native methionine or with further reprogramming with azide‐ and alkyne‐containing cognates. We further show macrocyclization and intermolecular modifications with these click handles, thus emphasizing the applicability of our method to current challenges in peptide and protein chemistry.
Collapse
Affiliation(s)
- Minglong Liu
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Vito Thijssen
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Seino A K Jongkees
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| |
Collapse
|
34
|
Liu M, Thijssen V, Jongkees SAK. Suppression of Formylation Provides an Alternative Approach to Vacant Codon Creation in Bacterial In Vitro Translation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Minglong Liu
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
| | - Vito Thijssen
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
| | - Seino A. K. Jongkees
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
| |
Collapse
|
35
|
Guerra-Castellano A, Márquez I, Pérez-Mejías G, Díaz-Quintana A, De la Rosa MA, Díaz-Moreno I. Post-Translational Modifications of Cytochrome c in Cell Life and Disease. Int J Mol Sci 2020; 21:E8483. [PMID: 33187249 PMCID: PMC7697256 DOI: 10.3390/ijms21228483] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/05/2020] [Accepted: 11/07/2020] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are the powerhouses of the cell, whilst their malfunction is related to several human pathologies, including neurodegenerative diseases, cardiovascular diseases, and various types of cancer. In mitochondrial metabolism, cytochrome c is a small soluble heme protein that acts as an essential redox carrier in the respiratory electron transport chain. However, cytochrome c is likewise an essential protein in the cytoplasm acting as an activator of programmed cell death. Such a dual role of cytochrome c in cell life and death is indeed fine-regulated by a wide variety of protein post-translational modifications. In this work, we show how these modifications can alter cytochrome c structure and functionality, thus emerging as a control mechanism of cell metabolism but also as a key element in development and prevention of pathologies.
Collapse
Affiliation(s)
| | | | | | | | | | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 49, 41092 Sevilla, Spain; (A.G.-C.); (I.M.); (G.P.-M.); (A.D.-Q.); (M.A.D.l.R.)
| |
Collapse
|
36
|
Kanoi BN, Nagaoka H, Morita M, Tsuboi T, Takashima E. Leveraging the wheat germ cell-free protein synthesis system to accelerate malaria vaccine development. Parasitol Int 2020; 80:102224. [PMID: 33137499 DOI: 10.1016/j.parint.2020.102224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/04/2020] [Accepted: 09/16/2020] [Indexed: 01/29/2023]
Abstract
Vaccines against infectious diseases have had great successes in the history of public health. Major breakthroughs have occurred in the development of vaccine-based interventions against viral and bacterial pathogens through the application of classical vaccine design strategies. In contrast the development of a malaria vaccine has been slow. Plasmodium falciparum malaria affects millions of people with nearly half of the world population at risk of infection. Decades of dedicated research has taught us that developing an effective vaccine will be time consuming, challenging, and expensive. Nevertheless, recent advancements such as the optimization of robust protein synthesis platforms, high-throughput immunoscreening approaches, reverse vaccinology, structural design of immunogens, lymphocyte repertoire sequencing, and the utilization of artificial intelligence, have renewed the prospects of an accelerated discovery of the key antigens in malaria. A deeper understanding of the major factors underlying the immunological and molecular mechanisms of malaria might provide a comprehensive approach to identifying novel and highly efficacious vaccines. In this review we discuss progress in novel antigen discoveries that leverage on the wheat germ cell-free protein synthesis system (WGCFS) to accelerate malaria vaccine development.
Collapse
Affiliation(s)
- Bernard N Kanoi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Hikaru Nagaoka
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Masayuki Morita
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Takafumi Tsuboi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan.
| |
Collapse
|
37
|
Drienovská I, Gajdoš M, Kindler A, Takhtehchian M, Darnhofer B, Birner-Gruenberger R, Dörr M, Bornscheuer UT, Kourist R. Folding Assessment of Incorporation of Noncanonical Amino Acids Facilitates Expansion of Functional-Group Diversity for Enzyme Engineering. Chemistry 2020; 26:12338-12342. [PMID: 32347609 PMCID: PMC7590180 DOI: 10.1002/chem.202002077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Indexed: 12/31/2022]
Abstract
Protein design is limited by the diversity of functional groups provided by the canonical protein „building blocks“. Incorporating noncanonical amino acids (ncAAs) into enzymes enables a dramatic expansion of their catalytic features. For this, quick identification of fully translated and correctly folded variants is decisive. Herein, we report the engineering of the enantioselectivity of an esterase utilizing several ncAAs. Key for the identification of active and soluble protein variants was the use of the split‐GFP method, which is crucial as it allows simple determination of the expression levels of enzyme variants with ncAA incorporations by fluorescence. Several identified variants led to improved enantioselectivity or even inverted enantiopreference in the kinetic resolution of ethyl 3‐phenylbutyrate.
Collapse
Affiliation(s)
- Ivana Drienovská
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Matúš Gajdoš
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Alexia Kindler
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Mahsa Takhtehchian
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Barbara Darnhofer
- Diagnostic and Research Institute of Patholoy, Diagnostic and Research Center of Molecular Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria.,Omics Center Graz, BioTechMed-Graz, Stiftingtalstraße 24, 8010, Graz, Austria
| | - Ruth Birner-Gruenberger
- Diagnostic and Research Institute of Patholoy, Diagnostic and Research Center of Molecular Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria.,Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060, Wien, Austria.,Omics Center Graz, BioTechMed-Graz, Stiftingtalstraße 24, 8010, Graz, Austria
| | - Mark Dörr
- Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Uwe T Bornscheuer
- Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Robert Kourist
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| |
Collapse
|
38
|
Abstract
This work details the use of amber suppression-mediated genetic incorporation of unnatural amino acids (UAAs), specifically p-azido-l-phenylalanine (pAzF) and p-acetyl-l-phenylalanine (pAcF), to develop site-specifically labeled antibody Fab fragments. These antibody fragment conjugates represent a novel class of imaging agents with optimal stability, efficacy, and pharmacological properties, which have demonstrated promising potential for probing and understanding the in vivo bio-distributions of protein targets of interest. This chapter provides general guidelines for preparing these Fab conjugates, and details of follow-up bioassays such as single-agent based positron emission tomography (PET) imaging of immune-checkpoint protein PD-L1, and the use of GCN4-mediated switchable antibody conjugates for near-infrared fluorescent imaging of cancer-related biomarkers.
Collapse
Affiliation(s)
- Robert Maloney
- Department of Chemistry, Temple University, Philadelphia, PA, United States
| | - Zakey Yusuf Buuh
- Department of Chemistry, Temple University, Philadelphia, PA, United States
| | - Yue Zhao
- Department of Chemistry, Temple University, Philadelphia, PA, United States
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, Philadelphia, PA, United States.
| |
Collapse
|
39
|
Ueki T, Walker DJF, Woodard TL, Nevin KP, Nonnenmann SS, Lovley DR. An Escherichia coli Chassis for Production of Electrically Conductive Protein Nanowires. ACS Synth Biol 2020; 9:647-654. [PMID: 32125829 DOI: 10.1021/acssynbio.9b00506] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Geobacter sulfurreducens' pilin-based electrically conductive protein nanowires (e-PNs) are a revolutionary electronic material. They offer novel options for electronic sensing applications and have the remarkable ability to harvest electrical energy from atmospheric humidity. However, technical constraints limit mass cultivation and genetic manipulation of G. sulfurreducens. Therefore, we designed a strain of Escherichia coli to express e-PNs by introducing a plasmid that contained an inducible operon with E. coli genes for type IV pili biogenesis machinery and a synthetic gene designed to yield a peptide monomer that could be assembled into e-PNs. The e-PNs expressed in E. coli and harvested with a simple filtration method had the same diameter (3 nm) and conductance as e-PNs expressed in G. sulfurreducens. These results, coupled with the robustness of E. coli for mass cultivation and the extensive E. coli toolbox for genetic manipulation, greatly expand the opportunities for large-scale fabrication of novel e-PNs.
Collapse
Affiliation(s)
- Toshiyuki Ueki
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Institute for Applied Life Sciences, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - David J. F. Walker
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Institute for Applied Life Sciences, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Trevor L. Woodard
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Kelly P. Nevin
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Stephen S. Nonnenmann
- Institute for Applied Life Sciences, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Department of Mechanical and Industrial Engineering, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Institute for Applied Life Sciences, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| |
Collapse
|
40
|
Seifried BM, Qi W, Yang YJ, Mai DJ, Puryear WB, Runstadler JA, Chen G, Olsen BD. Glycoprotein Mimics with Tunable Functionalization through Global Amino Acid Substitution and Copper Click Chemistry. Bioconjug Chem 2020; 31:554-566. [PMID: 32078297 DOI: 10.1021/acs.bioconjchem.9b00601] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Glycoproteins and their mimics are challenging to produce because of their large number of polysaccharide side chains that form a densely grafted protein-polysaccharide brush architecture. Herein a new approach to protein bioconjugate synthesis is demonstrated that can approach the functionalization densities of natural glycoproteins through oligosaccharide grafting. Global amino acid substitution is used to replace the methionine residues in a methionine-enriched elastin-like polypeptide with homopropargylglycine (HPG); the substitution was found to replace 93% of the 41 methionines in the protein sequence as well as broaden and increase the thermoresponsive transition. A series of saccharides were conjugated to the recombinant protein backbones through copper(I)-catalyzed alkyne-azide cycloaddition to determine reactivity trends, with 83-100% glycosylation of HPGs. Only an acetyl-protected sialyllactose moiety showed a lower level of 42% HPG glycosylation that is attributed to steric hindrance. The recombinant glycoproteins reproduced the key biofunctional properties of their natural counterparts such as viral inhibition and lectin binding.
Collapse
Affiliation(s)
- Brian M Seifried
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wenjing Qi
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200000, China
| | - Yun Jung Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Danielle J Mai
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wendy B Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, United States
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, United States
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200000, China
| | - Bradley D Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Macromolecular Science, Fudan University, Shanghai 200000, China
| |
Collapse
|
41
|
Ganguly HK, Basu G. Conformational landscape of substituted prolines. Biophys Rev 2020; 12:25-39. [PMID: 31953795 PMCID: PMC7040156 DOI: 10.1007/s12551-020-00621-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
The cyclic side chain of the amino acid proline confers unique conformational restraints on its backbone and side chain dihedral angles. This affects two equilibria-one at the backbone (cis/trans) and the other at the side chain (endo/exo). Substitutions on the proline ring impose additional steric and stereoelectronic effects that can further modulate both these equilibria, which in turn can also affect the backbone dihedral angle (ϕ, ψ) preferences. In this review, we have explored the conformational landscape of several termini capped mono-(2-, 3-, 4-, and 5-) substituted proline derivatives in the Cambridge Structural Database, correlating observed conformations with the nature of substituents and deciphering the underlying interactions for the observed structural biases. The impact of incorporating these derivatives within model peptides and proteins are also discussed for selected cases. Several of these substituents have been used to introduce bioorthogonal functionality and modulate structure-specific ligand recognition or used as spectroscopic probes. The incorporation of these diversely applicable functional groups, coupled with their ability to define an amino acid conformation via stereoelectronic effects, have a broad appeal among chemical biologists, molecular biophysicists, and medicinal chemists.
Collapse
Affiliation(s)
- Himal Kanti Ganguly
- Department of Biophysics, Bose Institute, P-1/12 CIT scheme VII M, Kolkata, 700054, India.
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT scheme VII M, Kolkata, 700054, India.
| |
Collapse
|
42
|
Sternisha SM, Whittington AC, Martinez Fiesco JA, Porter C, McCray MM, Logan T, Olivieri C, Veglia G, Steinbach PJ, Miller BG. Nanosecond-Timescale Dynamics and Conformational Heterogeneity in Human GCK Regulation and Disease. Biophys J 2020; 118:1109-1118. [PMID: 32023434 DOI: 10.1016/j.bpj.2019.12.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/11/2019] [Accepted: 12/19/2019] [Indexed: 11/25/2022] Open
Abstract
Human glucokinase (GCK) is the prototypic example of an emerging class of proteins with allosteric-like behavior that originates from intrinsic polypeptide dynamics. High-resolution NMR investigations of GCK have elucidated millisecond-timescale dynamics underlying allostery. In contrast, faster motions have remained underexplored, hindering the development of a comprehensive model of cooperativity. Here, we map nanosecond-timescale dynamics and structural heterogeneity in GCK using a combination of unnatural amino acid incorporation, time-resolved fluorescence, and 19F nuclear magnetic resonance spectroscopy. We find that a probe inserted within the enzyme's intrinsically disordered loop samples multiple conformations in the unliganded state. Glucose binding and disease-associated mutations that suppress cooperativity alter the number and/or relative population of these states. Together, the nanosecond kinetics characterized here and the millisecond motions known to be essential for cooperativity provide a dynamical framework with which we address the origins of cooperativity and the mechanism of activated, hyperinsulinemia-associated, noncooperative variants.
Collapse
Affiliation(s)
- Shawn M Sternisha
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida
| | - A Carl Whittington
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida; Department of Biological Science, Florida State University, Tallahassee, Florida
| | | | - Carol Porter
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida
| | - Malcolm M McCray
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida
| | - Timothy Logan
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida
| | - Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota; Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Peter J Steinbach
- Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, Maryland.
| | - Brian G Miller
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida.
| |
Collapse
|
43
|
Varanko A, Saha S, Chilkoti A. Recent trends in protein and peptide-based biomaterials for advanced drug delivery. Adv Drug Deliv Rev 2020; 156:133-187. [PMID: 32871201 PMCID: PMC7456198 DOI: 10.1016/j.addr.2020.08.008] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Engineering protein and peptide-based materials for drug delivery applications has gained momentum due to their biochemical and biophysical properties over synthetic materials, including biocompatibility, ease of synthesis and purification, tunability, scalability, and lack of toxicity. These biomolecules have been used to develop a host of drug delivery platforms, such as peptide- and protein-drug conjugates, injectable particles, and drug depots to deliver small molecule drugs, therapeutic proteins, and nucleic acids. In this review, we discuss progress in engineering the architecture and biological functions of peptide-based biomaterials -naturally derived, chemically synthesized and recombinant- with a focus on the molecular features that modulate their structure-function relationships for drug delivery.
Collapse
Affiliation(s)
| | | | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
| |
Collapse
|
44
|
Choi CP, Moon AS, Back PS, Jami‐Alahmadi Y, Vashisht AA, Wohlschlegel JA, Bradley PJ. A photoactivatable crosslinking system reveals protein interactions in the Toxoplasma gondii inner membrane complex. PLoS Biol 2019; 17:e3000475. [PMID: 31584943 PMCID: PMC6795473 DOI: 10.1371/journal.pbio.3000475] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/16/2019] [Accepted: 09/13/2019] [Indexed: 11/18/2022] Open
Abstract
The Toxoplasma gondii inner membrane complex (IMC) is an important organelle involved in parasite motility and replication. The IMC resides beneath the parasite’s plasma membrane and is composed of both membrane and cytoskeletal components. Although the protein composition of the IMC is becoming better understood, the protein–protein associations that enable proper functioning of the organelle remain largely unknown. Determining protein interactions in the IMC cytoskeletal network is particularly challenging, as disrupting the cytoskeleton requires conditions that disrupt protein complexes. To circumvent this problem, we demonstrate the application of a photoreactive unnatural amino acid (UAA) crosslinking system to capture protein interactions in the native intracellular environment. In addition to identifying binding partners, the UAA approach maps the binding interface of the bait protein used for crosslinking, providing structural information of the interacting proteins. We apply this technology to the essential IMC protein ILP1 and demonstrate that distinct regions of its C-terminal coiled-coil domain crosslink to the alveolins IMC3 and IMC6, as well as IMC27. We also show that the IMC3 C-terminal domain and the IMC6 N-terminal domain are necessary for binding to ILP1, further mapping interactions between ILP1 and the cytoskeleton. Together, this study develops a new approach to study protein–protein interactions in Toxoplasma and provides the first insight into the architecture of the cytoskeletal network of the apicomplexan IMC. The inner membrane complex of the human parasite Toxoplasma gondii is an important organelle involved in motility and replication. This study expands the genetic code of Toxoplasma, allowing the use of photoactivatable unnatural amino acids to uncover interactions within the apicomplexan inner membrane complex.
Collapse
Affiliation(s)
- Charles Paul Choi
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Andy Seong Moon
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Peter Sungmin Back
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Yasaman Jami‐Alahmadi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Ajay Amar Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - James Akira Wohlschlegel
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Peter John Bradley
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| |
Collapse
|
45
|
Micoli F, Del Bino L, Alfini R, Carboni F, Romano MR, Adamo R. Glycoconjugate vaccines: current approaches towards faster vaccine design. Expert Rev Vaccines 2019; 18:881-895. [PMID: 31475596 DOI: 10.1080/14760584.2019.1657012] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Introduction: Over the last decades, glycoconjugate vaccines have been proven to be a successful strategy to prevent infectious diseases. Many diseases remain to be controlled, especially in developing countries, and emerging antibiotic-resistant bacteria present an alarming public-health threat. The increasing complexity of future vaccines, and the need to accelerate development processes have triggered the development of faster approaches to glycoconjugate vaccines design. Areas covered: This review provides an overview of recent progress in glycoconjugation technologies toward faster vaccine design. Expert opinion: Among the different emerging approaches, glycoengineering has the potential to combine glycan assembly and conjugation to carrier systems (such as proteins or outer membrane vesicles) in one step, resulting in a simplified manufacturing process and fewer analytical controls. Chemical and enzymatic strategies, and their automation can facilitate glycoepitope identification for vaccine design. Other approaches, such as the liposomal encapsulation of polysaccharides, potentially enable fast and easy combination of numerous antigens in the same formulation. Additional progress is envisaged in the near future, and some of these systems still need to be further validated in humans. In parallel, new strategies are needed to accelerate the vaccine development process, including the associated clinical trials, up to vaccine release onto the market.
Collapse
Affiliation(s)
- Francesca Micoli
- Technology Platform, GSK Vaccines Institute for Global Health s.r.l , Siena , Italy
| | | | - Renzo Alfini
- Technology Platform, GSK Vaccines Institute for Global Health s.r.l , Siena , Italy
| | | | | | | |
Collapse
|
46
|
Li N, Zhang W, Li Y, Lin JM. Analysis of cellular biomolecules and behaviors using microfluidic chip and fluorescence method. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.05.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
47
|
Pérez‐Peinado C, Dias SA, Mendonça DA, Castanho MA, Veiga AS, Andreu D. Structural determinants conferring unusual long life in human serum to rattlesnake‐derived antimicrobial peptide Ctn[15‐34]. J Pept Sci 2019; 25:e3195. [DOI: 10.1002/psc.3195] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/07/2019] [Accepted: 05/13/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Clara Pérez‐Peinado
- Department of Experimental and Health ScienceUniversitat Pompeu Fabra, Barcelona Biomedical Research Park Barcelona 08003 Spain
| | - Susana A. Dias
- Instituto de Medicina Molecular, Faculdade de MedicinaUniversidade de Lisboa Lisbon 1649‐028 Portugal
| | - Diogo A. Mendonça
- Instituto de Medicina Molecular, Faculdade de MedicinaUniversidade de Lisboa Lisbon 1649‐028 Portugal
| | - Miguel A.R.B. Castanho
- Instituto de Medicina Molecular, Faculdade de MedicinaUniversidade de Lisboa Lisbon 1649‐028 Portugal
| | - Ana S. Veiga
- Instituto de Medicina Molecular, Faculdade de MedicinaUniversidade de Lisboa Lisbon 1649‐028 Portugal
| | - David Andreu
- Department of Experimental and Health ScienceUniversitat Pompeu Fabra, Barcelona Biomedical Research Park Barcelona 08003 Spain
| |
Collapse
|
48
|
Lee BS, Lee Y, Park J, Jeong BS, Jo M, Jung ST, Yoo TH. Construction of an immunotoxin via site-specific conjugation of anti-Her2 IgG and engineered Pseudomonas exotoxin A. J Biol Eng 2019; 13:56. [PMID: 31285754 PMCID: PMC6588878 DOI: 10.1186/s13036-019-0188-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 06/12/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Immunotoxins consisting of a toxin from bacteria or plants and a targeting module have been developed as potent anti-cancer therapeutics. The majority of them, especially those in preclinical or clinical testing stages, are fusion proteins of a toxin and antibody fragment. Immunotoxins based on full-length antibodies are less studied, even though the fragment crystallizable (Fc) domain plays an important role in regulating the concentration of immunoglobulin G (IgG) in the serum and in antibody-mediated immune responses against pathogens. RESULTS We devised a method to site-specifically conjugate IgG and another protein using a cysteine residue introduced into the IgG and a bio-orthogonally reactive unnatural amino acid incorporated into the other protein. The human epidermal growth factor receptor 2 (Her2)-targeting IgG, trastuzumab, was engineered to have an unpaired cysteine in the heavy chain, and an unnatural amino acid with the azido group was incorporated into an engineered Pseudomonas exotoxin A (PE24). The two protein molecules were conjugated site-specifically using a bifunctional linker having dibenzocyclooctyne and maleimide groups. Binding to Her2 and interaction with various Fc receptors of trastuzumab were not affected by the conjugation with PE24. The trastuzumab-PE24 conjugate was cytotoxic to Her2-overexpressing cell lines, which involved the inhibition of cellular protein synthesis due to the modification of elongation factor-2. CONCLUSIONS We constructed the site-specifically conjugated immunotoxin based on IgG and PE24, which induced target-specific cytotoxicity. To evaluate the molecule as a cancer therapeutic, animal studies are planned to assess tumor regression, half-life in blood, and in vivo immunogenicity. In addition, we expect that the site-specific conjugation method can be used to develop other antibody-protein conjugates for applications in therapeutics and diagnostics.
Collapse
Affiliation(s)
- Byeong Sung Lee
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
| | - Yumi Lee
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
| | - Jisoo Park
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
| | - Bo Seok Jeong
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
| | - Migyeong Jo
- Department of Applied Chemistry, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul, 02707 South Korea
| | - Sang Taek Jung
- Department of Biomedical Sciences, Graduate School of Medicine, Korea University, Seongbuk-gu, Seoul, 02841 South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
| |
Collapse
|
49
|
Hajek P, Bader A, Helmstetter F, Henke B, Arnold P, Beitz E. Cell-Free and Yeast-Based Production of the Malarial Lactate Transporter, PfFNT, Delivers Comparable Yield and Protein Quality. Front Pharmacol 2019; 10:375. [PMID: 31024323 PMCID: PMC6467934 DOI: 10.3389/fphar.2019.00375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/26/2019] [Indexed: 11/16/2022] Open
Abstract
Cell-free protein production is an attractive alternative to cell-based expression. Rapid results, small-volume reactions, irrelevance of protein toxicity, flexibility, and openness of the system are strong points in favor of the cell-free system. However, the in vitro situation lacks the cellular quality control machinery comprising e.g., the translocon for inserting membrane proteins into lipid bilayers, and chaperon-assisted protein degradation pathways. Here, we compare yield and protein quality of the lactate transporter, PfFNT, from malaria parasites when produced in Pichia pastoris yeast, or in an Escherichia coli S30-extract-based cell-free system. Besides solubilization and correct folding, PfFNT requires oligomerization into homopentamers. We assessed PfFNT folding/oligomerization and function by transmission electron microscopy imaging, transport assays, and binding of small-molecule inhibitors. For the latter, we used chromatography of the PfFNT-inhibitor complex with dual-wavelength detection, and biolayer interferometry. Our data show, that PfFNT possesses an intrinsic capability for assuming the correct fold, oligomerization pattern, and functionality during in vitro translation. This competence depended on the detergent present in the cell-free reaction. The choice of detergent further affected purification and inhibitor binding. In conclusion, in the presence of a suitable detergent, cell-free systems are very well capable of producing high quality membrane proteins.
Collapse
Affiliation(s)
- Philipp Hajek
- Department of Pharmaceutical and Medicinal Chemistry, Pharmaceutical Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Annika Bader
- Department of Pharmaceutical and Medicinal Chemistry, Pharmaceutical Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Folknand Helmstetter
- Department of Pharmaceutical and Medicinal Chemistry, Pharmaceutical Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Björn Henke
- Department of Pharmaceutical and Medicinal Chemistry, Pharmaceutical Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Philipp Arnold
- Anatomical Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Eric Beitz
- Department of Pharmaceutical and Medicinal Chemistry, Pharmaceutical Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| |
Collapse
|
50
|
A High-Throughput Platform for the Generation of Synthetic Ab Clones by Single-Strand Site-Directed Mutagenesis. Mol Biotechnol 2019; 61:410-420. [PMID: 30963479 DOI: 10.1007/s12033-019-00171-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Current developments in meta-data analysis and predictive computational models offer alternative routes for the identification of antibodies. In silico-based technologies and NGS data analysis from Ab phage-display selections offer expanded selections of Ab candidates. Accordingly, the identified de novo Abs with predicted selectivity for a target antigen must undergo rapid gene synthesis for downstream Ab characterizations. Here we describe a high-throughput strategy for the generation of synthetic Ab clones for expression as Fab proteins in Escherichia coli. Our approach utilizes simultaneous single-stranded site-directed mutagenesis of diversified Ab regions of a phagemid template with engineered complementary determining regions that contain multiple stop codon and restriction enzyme sites. Subsequently, we perform rapid screening of Ab DNA clones for correct gene assemblies by high-throughput Ab-phage protein expression screens. Identified sequences are corroborated by Sanger DNA sequencing analysis. In summary, our work describes a rapid and cost-effective platform for the high-throughput synthesis of synthetic Ab genes as Fab proteins for implementation into downstream protein validation pipelines.
Collapse
|