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Martínez DG, Hüttelmaier S, Bertoldo JB. Unveiling Druggable Pockets by Site-Specific Protein Modification: Beyond Antibody-Drug Conjugates. Front Chem 2020; 8:586942. [PMID: 33195086 PMCID: PMC7609475 DOI: 10.3389/fchem.2020.586942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/16/2020] [Indexed: 11/13/2022] Open
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Abstract
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease.
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3
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Loveridge EJ, Hroch L, Hughes RL, Williams T, Davies RL, Angelastro A, Luk LYP, Maglia G, Allemann RK. Reduction of Folate by Dihydrofolate Reductase from Thermotoga maritima. Biochemistry 2017; 56:1879-1886. [PMID: 28319664 DOI: 10.1021/acs.biochem.6b01268] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mammalian dihydrofolate reductases (DHFRs) catalyze the reduction of folate more efficiently than the equivalent bacterial enzymes do, despite typically having similar efficiencies for the reduction of their natural substrate, dihydrofolate. In contrast, we show here that DHFR from the hyperthermophilic bacterium Thermotoga maritima can catalyze reduction of folate to tetrahydrofolate with an efficiency similar to that of reduction of dihydrofolate under saturating conditions. Nuclear magnetic resonance and mass spectrometry experiments showed no evidence of the production of free dihydrofolate during either the EcDHFR- or TmDHFR-catalyzed reductions of folate, suggesting that both enzymes perform the two reduction steps without release of the partially reduced substrate. Our results imply that the reaction proceeds more efficiently in TmDHFR than in EcDHFR because the more open active site of TmDHFR facilitates protonation of folate. Because T. maritima lives under extreme conditions where tetrahydrofolate is particularly prone to oxidation, this ability to salvage folate may impart an advantage to the bacterium by minimizing the squandering of a valuable cofactor.
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Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K.,Department of Chemistry, Swansea University , Singleton Park, Swansea SA2 8PP, U.K
| | - Lukas Hroch
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K.,Department of Pharmaceutical Chemistry and Drug Control, Faculty of Pharmacy in Hradec Kralove, Charles University in Prague , Akademika Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic
| | - Robert L Hughes
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Thomas Williams
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Rhidian L Davies
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Antonio Angelastro
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Louis Y P Luk
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Giovanni Maglia
- School of Chemical Sciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K.,School of Chemical Sciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K
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4
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Shi Y, Long MJ, Rosenberg MM, Li S, Kobjack A, Lessans P, Coffey RT, Hedstrom L. Boc 3Arg-Linked Ligands Induce Degradation by Localizing Target Proteins to the 20S Proteasome. ACS Chem Biol 2016; 11:3328-3337. [PMID: 27704767 DOI: 10.1021/acschembio.6b00656] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Targeted protein degradation is a promising strategy for drug design and functional assessment. Several small molecule approaches have been developed that localize target proteins to ubiquitin ligases, inducing ubiquitination and subsequent degradation by the 26S proteasome. We discovered that the degradation of a target protein can also be induced by a recognition ligand linked to tert-butyl carbamate (Boc3)-protected arginine (B3A). Here, we show that this process requires the proteasome but does not involve ubiquitination of the target protein. B3A does not perturb the structure of the target protein; instead, a B3A-ligand stabilizes its target protein. B3A ligands stimulate activity of purified 20S proteasome, demonstrating that the tag binds directly to the 20S proteasome. Moreover, purified 20S proteasome is sufficient to degrade target proteins in the presence of their respective B3A-linked recognition ligands. These observations suggest a simple model for B3A-mediated degradation wherein the B3A tag localizes target proteins directly to the 20S proteasome. Thus, B3A ligands are the first example of a ubiquitin-free strategy for targeted protein degradation.
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Affiliation(s)
- Yuntao Shi
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Marcus J.C. Long
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Masha M. Rosenberg
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Shican Li
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Aimee Kobjack
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Philip Lessans
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Rory T. Coffey
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Lizbeth Hedstrom
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
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Gunnoo SB, Madder A. Chemical Protein Modification through Cysteine. Chembiochem 2016; 17:529-53. [DOI: 10.1002/cbic.201500667] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Smita B. Gunnoo
- Organic & Biomimetic Chemistry Research Group; Department of Organic and Macromolecular Chemistry; Ghent University; Krijgslaan 281 9000 Gent Belgium
| | - Annemieke Madder
- Organic & Biomimetic Chemistry Research Group; Department of Organic and Macromolecular Chemistry; Ghent University; Krijgslaan 281 9000 Gent Belgium
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2009-2010. MASS SPECTROMETRY REVIEWS 2015; 34:268-422. [PMID: 24863367 PMCID: PMC7168572 DOI: 10.1002/mas.21411] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/16/2013] [Accepted: 07/16/2013] [Indexed: 05/07/2023]
Abstract
This review is the sixth update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2010. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, arrays and fragmentation are covered in the first part of the review and applications to various structural typed constitutes the remainder. The main groups of compound that are discussed in this section are oligo and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Many of these applications are presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis.
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Affiliation(s)
- David J. Harvey
- Department of BiochemistryOxford Glycobiology InstituteUniversity of OxfordOxfordOX1 3QUUK
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Pandey BK, Enck S, Price JL. Stabilizing impact of N-glycosylation on the WW domain depends strongly on the Asn-GlcNAc linkage. ACS Chem Biol 2013; 8:2140-4. [PMID: 23937634 DOI: 10.1021/cb4004496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-glycans play important roles in many cellular processes and can increase protein conformational stability in specific structural contexts. Glycosylation (with a single GlcNAc) of the reverse turn sequence Phe-Yyy-Asn-Xxx-Thr at Asn stabilizes the Pin 1 WW domain by -0.85 ± 0.12 kcal mol(-1). Alternative methods exist for attaching carbohydrates to proteins; some occur naturally (e.g., the O-linkage), whereas others use chemoselective ligation reactions to mimic the natural N- or O-linkages. Here, we assess the energetic consequences of replacing the Asn linkage in the glycosylated WW domain with a Gln linkage, with two natural O-linkages, with two unnatural triazole linkages, and with an unnatural α-mercaptoacetamide linkage. Of these alternatives, only glycosylation of the triazole linkages stabilizes WW, and by a smaller amount than N-glycosylation, highlighting the need for caution when using triazole- or α-mercaptoacetamide-linked carbohydrates to mimic native N-glycans, especially where the impact of glycosylation on protein conformational stability is important.
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Affiliation(s)
- Brijesh K. Pandey
- Department of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
| | - Sebastian Enck
- Department of Chemistry and
Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California
92037, United States
| | - Joshua L. Price
- Department of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
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Guo J, Loveridge EJ, Luk LYP, Allemann RK. Effect of Dimerization on Dihydrofolate Reductase Catalysis. Biochemistry 2013; 52:3881-7. [DOI: 10.1021/bi4005073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jiannan Guo
- School of Chemistry and
Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff
CF10 3AT, United Kingdom
| | - E. Joel Loveridge
- School of Chemistry and
Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff
CF10 3AT, United Kingdom
| | - Louis Y. P. Luk
- School of Chemistry and
Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff
CF10 3AT, United Kingdom
| | - Rudolf K. Allemann
- School of Chemistry and
Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff
CF10 3AT, United Kingdom
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Stability mechanisms of a thermophilic laccase probed by molecular dynamics. PLoS One 2013; 8:e61985. [PMID: 23658618 PMCID: PMC3639223 DOI: 10.1371/journal.pone.0061985] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 03/15/2013] [Indexed: 11/25/2022] Open
Abstract
Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K), probing structural changes associated with enthalpy-entropy compensation. Approaching Topt (∼350 K) from 300 K, this change correlated with a beginning “unzipping” of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F− (but not Cl−) specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F− intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes.
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Zou S, Huang S, Kaleem I, Li C. N-Glycosylation enhances functional and structural stability of recombinant β-glucuronidase expressed in Pichia pastoris. J Biotechnol 2013; 164:75-81. [PMID: 23313889 DOI: 10.1016/j.jbiotec.2012.12.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 11/19/2022]
Abstract
Recombinant β-glucuronidase (GUS) expressed in Pichia pastoris GS115 is an important glycoprotein, encoded by a gene with four potential N-glycosylation sites. To investigate the impact of N-linked carbohydrate moieties on the stability of recombinant GUS, it was deglycosylated by peptide-N-glycosidase F (PNGase-F) under native conditions. The enzymatic activities of the glycosylated and deglycosylated GUS were compared under various conditions such as temperature, pH, organic solvents, detergents and chaotropic agent. The results demonstrated that the glycosylated GUS retained greater fraction of maximum enzymatic activity against various types of denaturants compared with the deglycosylated. The conformational stabilities of both GUS were analyzed by monitoring the unfolding equilibrium by using the denaturant guanidinium chloride (dn-HCl). The glycosylated GUS displayed a significant increase in its conformational stability than the deglycosylated counterpart. These results affirmed the key role of N-glycosylation on the structural and functional stability of β-glucuronidase and could have potential applications in the functional enhancement of industrial enzymes.
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Affiliation(s)
- Shuping Zou
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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