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Cano-Garrido O, Serna N, Unzueta U, Parladé E, Mangues R, Villaverde A, Vázquez E. Protein scaffolds in human clinics. Biotechnol Adv 2022; 61:108032. [PMID: 36089254 DOI: 10.1016/j.biotechadv.2022.108032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/30/2022] [Accepted: 09/03/2022] [Indexed: 11/02/2022]
Abstract
Fundamental clinical areas such as drug delivery and regenerative medicine require biocompatible materials as mechanically stable scaffolds or as nanoscale drug carriers. Among the wide set of emerging biomaterials, polypeptides offer enticing properties over alternative polymers, including full biocompatibility, biodegradability, precise interactivity, structural stability and conformational and functional versatility, all of them tunable by conventional protein engineering. However, proteins from non-human sources elicit immunotoxicities that might bottleneck further development and narrow their clinical applicability. In this context, selecting human proteins or developing humanized protein versions as building blocks is a strict demand to design non-immunogenic protein materials. We review here the expanding catalogue of human or humanized proteins tailored to execute different levels of scaffolding functions and how they can be engineered as self-assembling materials in form of oligomers, polymers or complex networks. In particular, we emphasize those that are under clinical development, revising their fields of applicability and how they have been adapted to offer, apart from mere mechanical support, highly refined functions and precise molecular interactions.
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Affiliation(s)
- Olivia Cano-Garrido
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain
| | - Naroa Serna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain
| | - Ugutz Unzueta
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute, 08916 Badalona (Barcelona), Spain
| | - Eloi Parladé
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain
| | - Ramón Mangues
- Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute, 08916 Badalona (Barcelona), Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain.
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain.
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Almohammed S, Fularz A, Kanoun MB, Goumri-Said S, Aljaafari A, Rodriguez BJ, Rice JH. Structural Transition-Induced Raman Enhancement in Bioinspired Diphenylalanine Peptide Nanotubes. ACS APPLIED MATERIALS & INTERFACES 2022; 14:12504-12514. [PMID: 35254049 PMCID: PMC8931724 DOI: 10.1021/acsami.1c22770] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Semiconducting materials are increasingly proposed as alternatives to noble metal nanomaterials to enhance Raman scattering. We demonstrate that bioinspired semiconducting diphenylalanine peptide nanotubes annealed through a reported structural transition can support Raman detection of 10-7 M concentrations for a range of molecules including mononucleotides. The enhancement is attributed to the introduction of electronic states below the conduction band that facilitate charge transfer to the analyte molecule. These results show that organic semiconductor-based materials can serve as platforms for enhanced Raman scattering for chemical sensing. As the sensor is metal-free, the enhancement is achieved without the introduction of electromagnetic surface-enhanced Raman spectroscopy.
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Affiliation(s)
- Sawsan Almohammed
- School
of Physics, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
- Conway
Institute of Biomolecular and Biomedical Research, University College,
Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - Agata Fularz
- School
of Physics, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - Mohammed Benali Kanoun
- Department
of Physics, College of Science, King Faisal
University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Souraya Goumri-Said
- Physics
Department, College of Science and General Studies, Alfaisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
| | - Abdullah Aljaafari
- Department
of Physics, College of Science, King Faisal
University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Brian J. Rodriguez
- School
of Physics, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
- Conway
Institute of Biomolecular and Biomedical Research, University College,
Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - James H. Rice
- School
of Physics, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
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Serna N, Pallarès V, Unzueta U, Garcia-Leon A, Voltà-Durán E, Sánchez-Chardi A, Parladé E, Rueda A, Casanova I, Falgàs A, Alba-Castellón L, Sierra J, Villaverde A, Vázquez E, Mangues R. Engineering non-antibody human proteins as efficient scaffolds for selective, receptor-targeted drug delivery. J Control Release 2022; 343:277-287. [PMID: 35051493 DOI: 10.1016/j.jconrel.2022.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/27/2021] [Accepted: 01/11/2022] [Indexed: 01/01/2023]
Abstract
Self-assembling non-immunoglobulin scaffold proteins are a promising class of nanoscale carriers for drug delivery and interesting alternatives to antibody-based carriers that are not sufficiently efficient in systemic administration. To exploit their potentialities in clinics, protein scaffolds need to be further tailored to confer appropriate targeting and to overcome their potential immunogenicity, short half-life in plasma and proteolytic degradation. We have here engineered three human scaffold proteins as drug carrier nanoparticles to target the cytokine receptor CXCR4, a tumoral cell surface marker of high clinical relevance. The capability of these scaffolds for the selective delivery of Monomethyl auristatin E has been comparatively evaluated in a disseminated mouse model of human, CXCR4+ acute myeloid leukemia. Monomethyl auristatin E is an ultra-potent anti-mitotic drug used against a range of hematological neoplasias, which because of its high toxicity is not currently administered as a free drug but as payload in antibody-drug conjugates. The protein nanoconjugates generated here offer a collective strength of simple manufacturing process, high proteolytic and structural stability and multivalent ligand receptor interactions that result in a highly efficient and selective delivery of the payload drug and in a potent anticancer effect. The approach shown here stresses this class of human scaffold proteins as promising alternatives to antibodies for targeted drug delivery in the rapidly evolving drug development landscape.
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Affiliation(s)
- Naroa Serna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain; Present address: Nanoligent SL. Edifici Eureka, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Victor Pallarès
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Mª Claret 167, 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC Campus Sant Pau), 08025 Barcelona, Spain
| | - Ugutz Unzueta
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Mª Claret 167, 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC Campus Sant Pau), 08025 Barcelona, Spain.
| | - Annabel Garcia-Leon
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Mª Claret 167, 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC Campus Sant Pau), 08025 Barcelona, Spain
| | - Eric Voltà-Durán
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain
| | - Alejandro Sánchez-Chardi
- Servei de Microscòpia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona. 08028 Barcelona, Spain
| | - Eloi Parladé
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain
| | - Ariana Rueda
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Mª Claret 167, 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC Campus Sant Pau), 08025 Barcelona, Spain
| | - Isolda Casanova
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Mª Claret 167, 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC Campus Sant Pau), 08025 Barcelona, Spain
| | - Aïda Falgàs
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Mª Claret 167, 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC Campus Sant Pau), 08025 Barcelona, Spain
| | - Lorena Alba-Castellón
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Mª Claret 167, 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC Campus Sant Pau), 08025 Barcelona, Spain
| | - Jorge Sierra
- Josep Carreras Leukaemia Research Institute (IJC Campus Sant Pau), 08025 Barcelona, Spain; Departament d'Hematologia, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain.
| | - Ramón Mangues
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Mª Claret 167, 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC Campus Sant Pau), 08025 Barcelona, Spain
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Identification and Characterization of an Affimer Affinity Reagent for the Detection of the cAMP Sensor, EPAC1. Cells 2021; 10:cells10092307. [PMID: 34571955 PMCID: PMC8465552 DOI: 10.3390/cells10092307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 01/15/2023] Open
Abstract
An exchange protein directly activated by cAMP 1 (EPAC1) is an intracellular sensor for cAMP that is involved in a wide variety of cellular and physiological processes in health and disease. However, reagents are lacking to study its association with intracellular cAMP nanodomains. Here, we use non-antibody Affimer protein scaffolds to develop isoform-selective protein binders of EPAC1. Phage-display screens were carried out against purified, biotinylated human recombinant EPAC1ΔDEP protein (amino acids 149–811), which identified five potential EPAC1-selective Affimer binders. Dot blots and indirect ELISA assays were next used to identify Affimer 780A as the top EPAC1 binder. Mutagenesis studies further revealed a potential interaction site for 780A within the EPAC1 cyclic nucleotide binding domain (CNBD). In addition, 780A was shown to co-precipitate EPAC1 from transfected cells and co-localize with both wild-type EPAC1 and a mis-targeting mutant of EPAC1(K212R), predominantly in perinuclear and cytosolic regions of cells, respectively. As a novel EPAC1-selective binder, 780A therefore has the potential to be used in future studies to further understand compartmentalization of the cAMP-EPAC1 signaling system.
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Tušar L, Usenik A, Turk B, Turk D. Mechanisms Applied by Protein Inhibitors to Inhibit Cysteine Proteases. Int J Mol Sci 2021; 22:ijms22030997. [PMID: 33498210 PMCID: PMC7863939 DOI: 10.3390/ijms22030997] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/13/2021] [Accepted: 01/16/2021] [Indexed: 02/07/2023] Open
Abstract
Protein inhibitors of proteases are an important tool of nature to regulate and control proteolysis in living organisms under physiological and pathological conditions. In this review, we analyzed the mechanisms of inhibition of cysteine proteases on the basis of structural information and compiled kinetic data. The gathered structural data indicate that the protein fold is not a major obstacle for the evolution of a protease inhibitor. It appears that nature can convert almost any starting fold into an inhibitor of a protease. In addition, there appears to be no general rule governing the inhibitory mechanism. The structural data make it clear that the “lock and key” mechanism is a historical concept with limited validity. However, the analysis suggests that the shape of the active site cleft of proteases imposes some restraints. When the S1 binding site is shaped as a pocket buried in the structure of protease, inhibitors can apply substrate-like binding mechanisms. In contrast, when the S1 binding site is in part exposed to solvent, the substrate-like inhibition cannot be employed. It appears that all proteases, with the exception of papain-like proteases, belong to the first group of proteases. Finally, we show a number of examples and provide hints on how to engineer protein inhibitors.
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Affiliation(s)
- Livija Tušar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Faculty of Chemistry, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
- Institute of Regenerative Medicine, I.M. Sechenov First Moscow State Medical University, Bol’shaya Pirogovskaya Ulitsa, 19c1, 119146 Moscow, Russia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
- Correspondence: ; Tel.: +386-1477-3857
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Ludwig SG, Kiyohara CL, Carlucci LA, Kisiela D, Sokurenko EV, Thomas WE. FimH as a scaffold for regulated molecular recognition. J Biol Eng 2021; 15:3. [PMID: 33436006 PMCID: PMC7805223 DOI: 10.1186/s13036-020-00253-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
Background Recognition proteins are critical in many biotechnology applications and would be even more useful if their binding could be regulated. The current gold standard for recognition molecules, antibodies, lacks convenient regulation. Alternative scaffolds can be used to build recognition proteins with new functionalities, including regulated recognition molecules. Here we test the use of the bacterial adhesin FimH as a scaffold for regulated molecular recognition. FimH binds to its native small molecule target mannose in a conformation-dependent manner that can be regulated by two types of noncompetitive regulation: allosteric and parasteric. Results We demonstrate that conformational regulation of FimH can be maintained even after reengineering the binding site to recognize the non-mannosylated targets nickel or Penta-His antibody, resulting in an up to 7-fold difference in KD between the two conformations. Moreover, both the allosteric and parasteric regulatory mechanisms native to FimH can be used to regulate binding to its new target. In one mutant, addition of the native ligand mannose parasterically improves the mutant’s affinity for Penta-His 4-fold, even as their epitopes overlap. In another mutant, the allosteric antibody mab21 reduces the mutant’s affinity for Penta-His 7-fold. The advantage of noncompetitive regulation is further illustrated by the ability of this allosteric regulator to induce 98% detachment of Penta-His, even with modest differences in affinity. Conclusions This illustrates the potential of FimH, with its deeply studied conformation-dependent binding, as a scaffold for conformationally regulated binding via multiple mechanisms. Supplementary Information The online version contains supplementary material available at 10.1186/s13036-020-00253-2.
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Affiliation(s)
- Shivani Gupta Ludwig
- Department of Bioengineering, University of Washington, 3720 15th Ave NE. Foege N430P, Box 355061, Seattle, USA
| | - Casey L Kiyohara
- Department of Bioengineering, University of Washington, 3720 15th Ave NE. Foege N430P, Box 355061, Seattle, USA
| | - Laura A Carlucci
- Department of Bioengineering, University of Washington, 3720 15th Ave NE. Foege N430P, Box 355061, Seattle, USA
| | - Dagmara Kisiela
- Department of Bioengineering, University of Washington, 3720 15th Ave NE. Foege N430P, Box 355061, Seattle, USA.,Department of Microbiology, University of Washington, HSB room J267a, Box 357735, Seattle, WA, USA
| | - Evgeni V Sokurenko
- Department of Bioengineering, University of Washington, 3720 15th Ave NE. Foege N430P, Box 355061, Seattle, USA.,Department of Microbiology, University of Washington, HSB room J267a, Box 357735, Seattle, WA, USA
| | - Wendy Evelyn Thomas
- Department of Bioengineering, University of Washington, 3720 15th Ave NE. Foege N430P, Box 355061, Seattle, USA.
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Zalar M, Golovanov AP. New Disulphide Bond in Cystatin-Based Protein Scaffold Prevents Domain-Swap-Mediated Oligomerization and Stabilizes the Functionally Active Form. ACS OMEGA 2019; 4:18248-18256. [PMID: 31720525 PMCID: PMC6844092 DOI: 10.1021/acsomega.9b02269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/18/2019] [Indexed: 05/13/2023]
Abstract
Peptide aptamers built using engineered scaffolds are a valuable alternative to monoclonal antibodies in many research applications because of their smaller size, versatility, specificity for chosen targets, and ease of production. However, inserting peptides needed for target binding may affect the aptamer structure, in turn compromising its activity. We have shown previously that a stefin A-based protein scaffold with AU1 and Myc peptide insertions (SQT-1C) spontaneously forms dimers and tetramers and that inserted loops mediate this process. In the present study, we show that SQT-1C forms tetramers by self-association of dimers and determine the kinetics of monomer-dimer and dimer-tetramer transitions. Using site-directed mutagenesis, we show that while slow domain swapping defines the rate of dimerization, conserved proline P80 is involved in the tetramerization process. We also demonstrate that the addition of a disulphide bond at the base of the engineered loop prevents domain swapping and dimer formation, also preventing subsequent tetramerization. Formation of SQT-1C oligomers compromises the presentation of inserted peptides for target molecule binding, diminishing aptamer activity; however, the introduction of the disulphide bond locking the monomeric state enables maximum specific aptamer activity, while also increasing its thermal and colloidal stability. We conclude that stabilizing scaffold proteins by adding disulphide bonds at peptide insertion sites might be a useful approach in preventing binding-epitope-driven oligomerization, enabling creation of very stable aptamers with maximum binding activity.
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Studies of the oligomerisation mechanism of a cystatin-based engineered protein scaffold. Sci Rep 2019; 9:9067. [PMID: 31227800 PMCID: PMC6588553 DOI: 10.1038/s41598-019-45565-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/06/2019] [Indexed: 12/11/2022] Open
Abstract
Engineered protein scaffolds are an alternative to monoclonal antibodies in research and drug design due to their small size, ease of production, versatility, and specificity for chosen targets. One key consideration when engineering such proteins is retaining the original scaffold structure and stability upon insertion of target-binding loops. SQT is a stefin A derived scaffold protein that was used as a model to study possible problems associated with solution behaviour of such aptamers. We used an SQT variant with AU1 and Myc insertion peptides (SQT-1C) to study the effect of peptide insertions on protein structure and oligomerisation. The X-ray structure of monomeric SQT-1C revealed a cystatin-like fold. Furthermore, we show that SQT-1C readily forms dimers and tetramers in solution. NMR revealed that these oligomers are symmetrical, with inserted loops comprising the interaction interface. Two possible mechanisms of oligomerisation are compared using molecular dynamics simulations, with domain swap oligomerisation being thermodynamically favoured. We show that retained secondary structure upon peptide insertion is not indicative of unaltered 3D structure and solution behaviour. Therefore, additional methods should be employed to comprehensively assess the consequences of peptide insertions in all aptamers, particularly as uncharacterized oligomerisation may alter binding epitope presentation and affect functional efficiency.
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Abstract
Dozens of studies have assessed the practical value of plant cystatins as ectopic inhibitors of Cys proteases in biological systems. The potential of these proteins in crop protection to control herbivorous pests and pathogens has been documented extensively over the past 25 years. Their usefulness to regulate endogenous Cys proteases in planta has also been considered recently, notably to implement novel traits of agronomic relevance in crops or to generate protease activity-depleted environments in plants or plant cells used as bioreactors for recombinant proteins. After a brief update on the basic structural characteristics of plant cystatins, we summarize recent advances on the use of these proteins in plant biotechnology. Attention is also paid to the molecular improvement of their structural properties for the improvement of their protease inhibitory effects or the fine-tuning of their biological target range.
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10
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Bratovš A, Kramer L, Mikhaylov G, Vasiljeva O, Turk B. Stefin A-functionalized liposomes as a system for cathepsins S and L-targeted drug delivery. Biochimie 2019; 166:94-102. [PMID: 31163196 DOI: 10.1016/j.biochi.2019.05.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/30/2019] [Indexed: 01/26/2023]
Abstract
Proteolytic activity in the tumor microenvironment is one of the key elements supporting tumor development and metastasis. One of the key families of proteases that are overexpressed in various types of cancer and implicated in different stages of tumor progression are cysteine cathepsins. Among them, cathepsins S and L can be secreted into the tumor microenvironment by tumor and/or immune cells, making them promising drug delivery targets. Here we present a new system for cathepsin S/L targeting using a liposomal drug carrier system functionalized with the endogenous cysteine cathepsin inhibitor, stefin A. The selective targeting of cathepsins by stefin A-conjugated liposomes was confirmed in vitro and in vivo, demonstrating the potential of this approach for cancer diagnosis and treatment.
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Affiliation(s)
- Andreja Bratovš
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Jozef Stefan International Postgraduate School, Jamova 39, Sl-1000 Ljubljana, Slovenia
| | - Lovro Kramer
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Georgy Mikhaylov
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Olga Vasiljeva
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, Večna Pot 113, University of Ljubljana, SI-1000 Ljubljana, Slovenia.
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11
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Tullius R, Platt GW, Khorashad LK, Gadegaard N, Lapthorn AJ, Rotello VM, Cooke G, Barron LD, Govorov AO, Karimullah AS, Kadodwala M. Superchiral Plasmonic Phase Sensitivity for Fingerprinting of Protein Interface Structure. ACS NANO 2017; 11:12049-12056. [PMID: 29220155 PMCID: PMC6034627 DOI: 10.1021/acsnano.7b04698] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The structure adopted by biomaterials, such as proteins, at interfaces is a crucial parameter in a range of important biological problems. It is a critical property in defining the functionality of cell/bacterial membranes and biofilms (i.e., in antibiotic-resistant infections) and the exploitation of immobilized enzymes in biocatalysis. The intrinsically small quantities of materials at interfaces precludes the application of conventional spectroscopic phenomena routinely used for (bio)structural analysis due to a lack of sensitivity. We show that the interaction of proteins with superchiral fields induces asymmetric changes in retardation phase effects of excited bright and dark modes of a chiral plasmonic nanostructure. Phase retardations are obtained by a simple procedure, which involves fitting the line shape of resonances in the reflectance spectra. These interference effects provide fingerprints that are an incisive probe of the structure of interfacial biomolecules. Using these fingerprints, layers composed of structurally related proteins with differing geometries can be discriminated. Thus, we demonstrate a powerful tool for the bioanalytical toolbox.
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Affiliation(s)
- Ryan Tullius
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Geoffrey W. Platt
- Avacta Life Sciences, Ash Way, Thorp Arch Estate, Wetherby, LS23 7FA, UK
| | | | - Nikolaj Gadegaard
- School of Engineering, Rankine Building, University of Glasgow, Glasgow, G12 8LT, UK
| | - Adrian J. Lapthorn
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Vincent M. Rotello
- Department of Chemistry, 710 Nt. Pleasant Street, University of Massachusetts Amherst, MA 01003, USA
| | - Graeme Cooke
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Laurence D. Barron
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - Affar S. Karimullah
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK
- School of Engineering, Rankine Building, University of Glasgow, Glasgow, G12 8LT, UK
| | - Malcolm Kadodwala
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ, UK
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12
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Bedford R, Tiede C, Hughes R, Curd A, McPherson MJ, Peckham M, Tomlinson DC. Alternative reagents to antibodies in imaging applications. Biophys Rev 2017; 9:299-308. [PMID: 28752365 PMCID: PMC5578921 DOI: 10.1007/s12551-017-0278-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/06/2017] [Indexed: 12/21/2022] Open
Abstract
Antibodies have been indispensable tools in molecular biology, biochemistry and medical research. However, a number of issues surrounding validation, specificity and batch variation of commercially available antibodies have prompted research groups to develop novel non-antibody binding reagents. The ability to select highly specific monoclonal non-antibody binding proteins without the need for animals, the ease of production and the ability to site-directly label has enabled a wide variety of applications to be tested, including imaging. In this review, we discuss the success of a number of non-antibody reagents in imaging applications, including the recently reported Affimer.
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Affiliation(s)
- R Bedford
- School of Molecular and Cellular Biology, Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - C Tiede
- School of Molecular and Cellular Biology, Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - R Hughes
- School of Molecular and Cellular Biology, Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - A Curd
- School of Molecular and Cellular Biology, Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - M J McPherson
- School of Molecular and Cellular Biology, Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Michelle Peckham
- School of Molecular and Cellular Biology, Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.
| | - Darren C Tomlinson
- School of Molecular and Cellular Biology, Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.
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13
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Abstract
Biosensors that depend on a physical or chemical measurement can be adversely affected by non-specific interactions. For example, a biosensor designed to measure specifically the levels of a rare analyte can give false positive results if there is even a small amount of interaction with a highly abundant but irrelevant molecule. To overcome this limitation, the biosensor community has frequently turned to antibody molecules as recognition elements because they are renowned for their exquisite specificity. Unfortunately antibodies can often fail when immobilised on inorganic surfaces, and alternative biological recognition elements are needed. This article reviews the available non-antibody-binding proteins that have been successfully used in electrical and micro-mechanical biosensor platforms.
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14
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Rossmann M, J Greive S, Moschetti T, Dinan M, Hyvönen M. Development of a multipurpose scaffold for the display of peptide loops. Protein Eng Des Sel 2017; 30:419-430. [PMID: 28444399 PMCID: PMC5897841 DOI: 10.1093/protein/gzx017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 02/26/2017] [Accepted: 03/28/2017] [Indexed: 12/20/2022] Open
Abstract
Protein-protein interactions (PPIs) determine a wide range of biological processes and analysis of these dynamic networks is increasingly becoming a mandatory tool for studying protein function. Using the globular ATPase domain of recombinase RadA as a scaffold, we have developed a peptide display system (RAD display), which allows for the presentation of target peptides, protein domains or full-length proteins and their rapid recombinant production in bacteria. The design of the RAD display system includes differently tagged versions of the scaffold, which allows for flexibility in the protein purification method, and chemical coupling for small molecule labeling or surface immobilization. When combined with the significant thermal stability of the RadA protein, these features create a versatile multipurpose scaffold system. Using various orthogonal biophysical techniques, we show that peptides displayed on the scaffold bind to their natural targets in a fashion similar to linear parent peptides. We use the examples of CK2β/CK2α kinase and TPX2/Aurora A kinase protein complexes to demonstrate that the peptide displayed by the RAD scaffold can be used in PPI studies with the same binding efficacy but at lower costs compared with their linear synthetic counterparts.
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Affiliation(s)
- Maxim Rossmann
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Tommaso Moschetti
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Michael Dinan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK. Correspondence:
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15
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Dias AM, Roque AC. The future of protein scaffolds as affinity reagents for purification. Biotechnol Bioeng 2016; 114:481-491. [DOI: 10.1002/bit.26090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Ana M.G.C. Dias
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Campus Caparica Caparica 2829-516 Portugal
| | - Ana C.A. Roque
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Campus Caparica Caparica 2829-516 Portugal
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16
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Kyle HF, Wickson KF, Stott J, Burslem GM, Breeze AL, Tiede C, Tomlinson DC, Warriner SL, Nelson A, Wilson AJ, Edwards TA. Exploration of the HIF-1α/p300 interface using peptide and Adhiron phage display technologies. MOLECULAR BIOSYSTEMS 2016; 11:2738-49. [PMID: 26135796 DOI: 10.1039/c5mb00284b] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The HIF-1α/p300 protein-protein interaction plays a key role in tumor metabolism and thus represents a high value target for anticancer drug-development. Although several studies have identified inhibitor candidates using rationale design, more detailed understanding of the interaction and binding interface is necessary to inform development of superior inhibitors. In this work, we report a detailed biophysical analysis of the native interaction with both peptide and Adhiron phage display experiments to identify novel binding motifs and binding regions of the surface of p300 to inform future inhibitor design.
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Affiliation(s)
- Hannah F Kyle
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
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17
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Stadler LKJ, Tomlinson DC, Lee T, Knowles MA, Ko Ferrigno P. The use of a neutral peptide aptamer scaffold to anchor BH3 peptides constitutes a viable approach to studying their function. Cell Death Dis 2014; 5:e1037. [PMID: 24481451 PMCID: PMC4040713 DOI: 10.1038/cddis.2013.564] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 11/26/2013] [Accepted: 11/27/2013] [Indexed: 11/11/2022]
Abstract
The B-cell CLL/lymphoma-2 (Bcl-2) family of proteins are important regulators of the intrinsic pathway of apoptosis, and their interactions, driven by Bcl-2 homology (BH) domains, are of great interest in cancer research. Particularly, the BH3 domain is of clinical relevance, as it promotes apoptosis through activation of Bcl-2-associated x protein (Bax) and Bcl-2 antagonist killer (Bak), as well as by antagonising the anti-apoptotic Bcl-2 family members. Although investigated extensively in vitro, the study of the BH3 domain alone inside cells is more problematic because of diminished secondary structure of the unconstrained peptide and a lack of stability. In this study, we report the successful use of a novel peptide aptamer scaffold – Stefin A quadruple mutant – to anchor and present the BH3 domains from Bcl-2-interacting mediator of cell death (Bim), p53 upregulated modulator of apoptosis (Puma), Bcl-2-associated death promoter (Bad) and Noxa, and demonstrate its usefulness in the study of the BH3 domains in vivo. When expressed intracellularly, anchored BH3 peptides exhibit much the same binding specificities previously established in vitro, however, we find that, at endogenous expression levels, Bcl-2 does not bind to any of the anchored BH3 domains tested. Nonetheless, when expressed inside cells the anchored PUMA and Bim BH3 α-helices powerfully induce cell death in the absence of efficient targeting to the mitochondrial membrane, whereas the Noxa helix requires a membrane insertion domain in order to kill Mcl-1-dependent myeloma cells. Finally, the binding of the Bim BH3 peptide to Bax was the only interaction with a pro-apoptotic effector protein observed in this study.
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Affiliation(s)
- L K J Stadler
- 1] Section of Experimental Therapeutics, Leeds LS9 7TF, UK [2] Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - D C Tomlinson
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - T Lee
- Section of Experimental Therapeutics, Leeds LS9 7TF, UK
| | - M A Knowles
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - P Ko Ferrigno
- Section of Experimental Therapeutics, Leeds LS9 7TF, UK
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18
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Luo X, Davis JJ. Electrical biosensors and the label free detection of protein disease biomarkers. Chem Soc Rev 2013; 42:5944-62. [DOI: 10.1039/c3cs60077g] [Citation(s) in RCA: 331] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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19
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Johnson A, Song Q, Ko Ferrigno P, Bueno PR, Davis JJ. Sensitive Affimer and Antibody Based Impedimetric Label-Free Assays for C-Reactive Protein. Anal Chem 2012; 84:6553-60. [DOI: 10.1021/ac300835b] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Anthony Johnson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1
3TA, United Kingdom
| | - Qifeng Song
- Wellcome
Trust/EPSRC/Leeds Medical
Engineering Centre, Leeds Institute of Molecular Medicine, Wellcome
Trust Brenner Building, St James’s University Hospital, Leeds LS9 7TF, United Kingdom
| | - Paul Ko Ferrigno
- Wellcome
Trust/EPSRC/Leeds Medical
Engineering Centre, Leeds Institute of Molecular Medicine, Wellcome
Trust Brenner Building, St James’s University Hospital, Leeds LS9 7TF, United Kingdom
| | - Paulo R. Bueno
- Instituto de Química (Institute
of Chemistry, Physical Chemistry Department), Universidade Estadual Paulista (São Paulo State University, UNESP), CP 355, 14800-900, Araraquara, São Paulo, Brazil
| | - Jason J. Davis
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1
3TA, United Kingdom
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20
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Tedeschi F, Di Maro A, Facchiano A, Costantini S, Chambery A, Bruni N, Capuzzi V, Ficca AG, Poerio E. Wheat Subtilisin/Chymotrypsin Inhibitor (WSCI) as a scaffold for novel serine protease inhibitors with a given specificity. MOLECULAR BIOSYSTEMS 2012; 8:3335-43. [DOI: 10.1039/c2mb25320h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Mascini M, Palchetti I, Tombelli S. Nucleic acid and peptide aptamers: fundamentals and bioanalytical aspects. Angew Chem Int Ed Engl 2011; 51:1316-32. [PMID: 22213382 DOI: 10.1002/anie.201006630] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Indexed: 12/11/2022]
Abstract
In recent years new nucleic acid and protein-based combinatorial molecules have attracted the attention of researchers working in various areas of science, ranging from medicine to analytical chemistry. These molecules, called aptamers, have been proposed as alternatives to antibodies in many different applications. The aim of this Review is to illustrate the peculiarities of these combinatorial molecules which have initially been explored for their importance in molecular medicine, but have enormous potential in other biotechnological fields historically dominated by antibodies, such as bioassays. A description of these molecules is given, and the methods for their selection and production are also summarized. Moreover, critical aspects related to these molecules are discussed.
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Affiliation(s)
- Marco Mascini
- Dipartimento di Chimica Ugo Schiff, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
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22
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Mascini M, Palchetti I, Tombelli S. Nucleinsäure- und Peptidaptamere: Grundlagen und bioanalytische Aspekte. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006630] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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23
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Stadler LKJ, Hoffmann T, Tomlinson DC, Song Q, Lee T, Busby M, Nyathi Y, Gendra E, Tiede C, Flanagan K, Cockell SJ, Wipat A, Harwood C, Wagner SD, Knowles MA, Davis JJ, Keegan N, Ferrigno PK. Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant. Protein Eng Des Sel 2011; 24:751-63. [PMID: 21616931 DOI: 10.1093/protein/gzr019] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Constrained binding peptides (peptide aptamers) may serve as tools to explore protein conformations and disrupt protein-protein interactions. The quality of the protein scaffold, by which the binding peptide is constrained and presented, is of crucial importance. SQT (Stefin A Quadruple Mutant-Tracy) is our most recent development in the Stefin A-derived scaffold series. Stefin A naturally uses three surfaces to interact with its targets. SQT tolerates peptide insertions at all three positions. Peptide aptamers in the SQT scaffold can be expressed in bacterial, yeast and human cells, and displayed as a fusion to truncated pIII on phage. Peptides that bind to CDK2 can show improved binding in protein microarrays when presented by the SQT scaffold. Yeast two-hybrid libraries have been screened for binders to the POZ domain of BCL-6 and to a peptide derived from PBP2', specific to methicillin-resistant Staphylococcus aureus. Presentation of the Noxa BH3 helix by SQT allows specific interaction with Mcl-1 in human cells. Together, our results show that Stefin A-derived scaffolds, including SQT, can be used for a variety of applications in cellular and molecular biology. We will henceforth refer to Stefin A-derived engineered proteins as Scannins.
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Affiliation(s)
- Lukas Kurt Josef Stadler
- Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St James's University Hospital, Leeds, UK
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24
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Song Q, Stadler LKJ, Peng J, Ko Ferrigno P. Peptide aptamer microarrays: bridging the bio-detector interface. Faraday Discuss 2011; 149:79-92; discussion 137-57. [PMID: 21413175 DOI: 10.1039/c005376g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the near future, personalised medicine and phase-0 trials will require that clinical practitioners move from the "one biomarker per disease" paradigm to the use of molecular signatures of disease for diagnosis and the prediction of a patient's response to treatment. These signatures will be composed of biomarkers specific to the disease, and will include over-expression of normal protein from a gene that does not carry a mutation; loss of expression of an essential protein; expression of a protein from a mutant gene; and metabolites whose levels are altered in disease. Surrogates for protein expression, such as alterations in the messenger RNA that encode for them, have already proved their value. The next challenge, then, in clinical biosensing is to enable the multiplexed detection of protein biomarkers, and perhaps the multiplexed detection of mixed biomarkers (metabolites, RNA and proteins) all in a single test. Given the plethora of available antibodies specific for biomarkers, why is this not already happening? We believe that the limitation lies in the nature of the antibody molecule itself, and especially the fact that antibodies have evolved to function in solution, while most diagnostic tests take place at a surface. We have accordingly turned to the design of alternative antibodies, and have identified a protein that appears to be unusually stable on surfaces. The new, non-antibody, scaffold protein is derived from human Stefin A, a natural inhibitor of the cathepsin family of proteases. We have engineered this protein so that it lacks natural binding partners, and introduced a series of new binding surfaces through randomisation or directed replacement of the surfaces used by Stefin A to bind to cathepsins. Our new probes show exquisite specificity and binding affinities comparable to antibodies, and can be used to probe biology in intact cells. More importantly, together and in collaboration with other groups in Chemistry or Engineering Departments, we have shown that these designer proteins can be used in optical detection of labelled target proteins from whole cell lysates in a highly multiplexed microarray format, as well as in label-free detection of unlabelled proteins using surface plasmon resonance, QCM, microcantilevers and using electrochemical assays on gold electrodes. We believe that the combination of optimised surface chemistry, robust and combinatorial designer biological probes and novel, robust and sensitive detection technologies will enable, in the near future, the introduction of multiplexed biomarker detection in the clinical setting, most likely in cancer where multiple biomarkers are known, but probes are still lacking.
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Affiliation(s)
- Qifeng Song
- Section of Experimental Therapeutics, Wellcome Trust Brenner Building, St James's University Hospital, Beckett Street, Leeds, LS9 7TF
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25
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Optimisation of a multivalent Strep tag for protein detection. Biophys Chem 2010; 152:170-7. [PMID: 20970240 DOI: 10.1016/j.bpc.2010.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 09/20/2010] [Accepted: 09/20/2010] [Indexed: 02/05/2023]
Abstract
The Strep tag is a peptide sequence that is able to mimic biotin's ability to bind to streptavidin. Sequences of Strep tags from 0 to 5 have been appended to the N-terminus of a model protein, the Stefin A Quadruple Mutant (SQM) peptide aptamer scaffold, and the recombinant fusion proteins expressed. The affinities of the proteins for streptavidin have been assessed as a function of the number of tags inserted using a variety of labelled and label-free bioanalytical and surface based methods (Western blots, microarray assays and surface plasmon resonance spectroscopy). The binding affinity increases with the number of tags across all assays, reaching nanomolar levels with 5 inserts, an observation assigned to a progressive increase in the probability of a binding interaction occurring. In addition a novel interfacial FRET based assay has been developed for generic Strep tag interactions, which utilises a conventional microarray scanner and bypasses the requirement for expensive lifetime imaging equipment. By labelling both the tagged StrepX-SQM(2) and streptavidin targets, the conjugate is primed for label-free FRET based displacement assays.
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