1
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Du Y, Kobashigawa Y, Okazaki K, Ogawa M, Kawaguchi T, Sato T, Morioka H. Structure-based design, biophysical characterization, and biochemical application of the heterodimeric affinity purification tag based on the Schistosoma japonicum glutathione-S-transferase (SjGST) homodimer. J Biochem 2024; 176:69-80. [PMID: 38471515 DOI: 10.1093/jb/mvae028] [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: 11/21/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024] Open
Abstract
Schistosoma japonicum glutathione-S-transferase (SjGST), the so-called GST-tag, is one of the most widely used protein tags for the purification of recombinant proteins by affinity chromatography. Attachment of SjGST enables the purification of a protein of interest (POI) using commercially available glutathione-immobilizing resins. Here we produced an SjGST mutant pair that forms heterodimers by adjusting the salt bridge pairs in the homodimer interface of SjGST. An MD study confirmed that the SjGST mutant pair did not disrupt the heterodimer formation. The modified SjGST protein pair coexpressed in Escherichia coli was purified by glutathione-immobilized resin. The stability of the heterodimeric form of the SjGST mutant pair was further confirmed by size exclusion chromatography. Surface plasmon resonance measurements unveiled the selective formation of heterodimers within the pair, accompanied by a significant suppression of homodimerization. The heterodimeric SjGST exhibited enzymatic activity in assays employing a commercially available fluorescent substrate. By fusing one member of the heterodimeric SjGST pair with a fluorescent protein and the other with the POI, we were able to conveniently and sensitively detect protein-protein interactions using fluorescence spectroscopy in the pull-down assays. Thus, utilization of the heterodimeric SjGST would be a useful tag for protein science.
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Affiliation(s)
- Yan Du
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Yoshihiro Kobashigawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Kyo Okazaki
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Mizuki Ogawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Tomoyuki Kawaguchi
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Takashi Sato
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Hiroshi Morioka
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
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2
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Douzi B. Surface Plasmon Resonance: A Sensitive Tool to Study Protein-Protein Interactions. Methods Mol Biol 2024; 2715:363-382. [PMID: 37930540 DOI: 10.1007/978-1-0716-3445-5_23] [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: 11/07/2023]
Abstract
Surface plasmon resonance (SPR) is one of the most commonly used techniques to study protein-protein interactions. The main advantage of SPR is the ability of measuring binding affinities and association/dissociation kinetics of complexes in real time, in a label-free environment, and using relatively small quantities of materials. The method is based on the immobilization of one of the binding partners, called the "ligand," on a dedicated sensor surface. Immobilization is followed by the injection of the other partner, called the "analyte," over the surface containing the ligand. The binding is monitored by following changes in the refractive index of the medium close to the sensor surface upon injection of the analyte. During the last 15 years, SPR has been intensively used in the study of bacterial secretion systems due to its ability of detecting highly dynamic complexes, which are difficult to investigate by other techniques. This chapter will guide users in setting up SPR experiments in order to identify protein complexes and to assess their binding affinity and/or kinetics. It will include detailed protocols for (i) immobilization of proteins with the amine coupling capture method, (ii) analyte-binding analysis, (iii) affinity/kinetics measurements, and (iv) data analysis.
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3
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Paiva ACF, Lemos AR, Busse P, Martins MT, Silva DO, Freitas MC, Santos SP, Freire F, Barrey EJ, Manival X, Koetzner L, Heinrich T, Wegener A, Grädler U, Bandeiras TM, Schwarz D, Sousa PMF. Extract2Chip-Bypassing Protein Purification in Drug Discovery Using Surface Plasmon Resonance. BIOSENSORS 2023; 13:913. [PMID: 37887106 PMCID: PMC10605449 DOI: 10.3390/bios13100913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/24/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
Modern drug discovery relies on combinatorial screening campaigns to find drug molecules targeting specific disease-associated proteins. The success of such campaigns often relies on functional and structural information of the selected therapeutic target, only achievable once its purification is mastered. With the aim of bypassing the protein purification process to gain insights on the druggability, ligand binding, and/or characterization of protein-protein interactions, herein, we describe the Extract2Chip method. This approach builds on the immobilization of site-specific biotinylated proteins of interest, directly from cellular extracts, on avidin-coated sensor chips to allow for the characterization of molecular interactions via surface plasmon resonance (SPR). The developed method was initially validated using Cyclophilin D (CypD) and subsequently applied to other drug discovery projects in which the targets of interest were difficult to express, purify, and crystallize. Extract2Chip was successfully applied to the characterization of Yes-associated protein (YAP): Transcriptional enhancer factor TEF (TEAD1) protein-protein interaction inhibitors, in the validation of a ternary complex assembly composed of Dyskerin pseudouridine synthase 1 (DKC1) and RuvBL1/RuvBL2, and in the establishment of a fast-screening platform to select the most suitable NUAK family SNF1-like kinase 2 (NUAK2) surrogate for binding and structural studies. The described method paves the way for a potential revival of the many drug discovery campaigns that have failed to deliver due to the lack of suitable and sufficient protein supply.
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Affiliation(s)
- Ana C. F. Paiva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ana R. Lemos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Philipp Busse
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Madalena T. Martins
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
| | - Diana O. Silva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Micael C. Freitas
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Sandra P. Santos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Filipe Freire
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Evelyne J. Barrey
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Xavier Manival
- IMoPA, CNRS, Université de Lorraine, F-54000 Nancy, France;
| | - Lisa Koetzner
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Timo Heinrich
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Ansgar Wegener
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Ulrich Grädler
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Tiago M. Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Daniel Schwarz
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Pedro M. F. Sousa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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4
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Alassiri M, Lai JY, Ch'ng ACW, Choong YS, Alanazi A, Lim TS. Subtractive panning for the isolation of monoclonal PEPITEM peptide antibody by phage display. Sci Rep 2023; 13:13627. [PMID: 37604859 PMCID: PMC10442400 DOI: 10.1038/s41598-023-40630-7] [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: 03/28/2023] [Accepted: 08/14/2023] [Indexed: 08/23/2023] Open
Abstract
Antibody phage display is a key tool for the development of monoclonal antibodies against various targets. However, the development of anti-peptide antibodies is a challenging process due to the small size of peptides for binding. This makes anchoring of peptides a preferred approach for panning experiments. A common approach is by using streptavidin as the anchor protein to present biotinylated peptides for panning. Here, we propose the use of recombinant expression of the target peptide and an immunogenic protein as a fusion for panning. The peptide inhibitor of trans-endothelial migration (PEPITEM) peptide sequence was fused to the Mycobacterium tuberculosis (Mtb) α-crystalline (AC) as an anchor protein. The panning process was carried out by subtractive selection of the antibody library against the AC protein first, followed by binding to the library to PEPITEM fused AC (PEPI-AC). A unique monoclonal scFv antibodies with good specificity were identified. In conclusion, the use of an alternative anchor protein to present the peptide sequence coupled with subtractive panning allows for the identification of unique monoclonal antibodies against a peptide target.
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Affiliation(s)
- Mohammed Alassiri
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Kingdom of Saudi Arabia.
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Kingdom of Saudi Arabia.
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of the National Guard - Health Affairs, Riyadh, Kingdom of Saudi Arabia.
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Asma Alanazi
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Kingdom of Saudi Arabia
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Kingdom of Saudi Arabia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia.
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5
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Dégardin M, Gaudreault J, Oliverio R, Serafin B, Forest-Nault C, Liberelle B, De Crescenzo G. Grafting Strategies of Oxidation-Prone Coiled-Coil Peptides for Protein Capture in Bioassays: Impact of Orientation and the Oxidation State. ACS OMEGA 2023; 8:28301-28313. [PMID: 37576632 PMCID: PMC10413464 DOI: 10.1021/acsomega.3c02172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/14/2023] [Indexed: 08/15/2023]
Abstract
Many biomedical and biosensing applications require functionalization of surfaces with proteins. To this end, the E/K coiled-coil peptide heterodimeric system has been shown to be advantageous. First, Kcoil peptides are covalently grafted onto a given surface. Ecoil-tagged proteins can then be non-covalently captured via a specific interaction with their Kcoil partners. Previously, oriented Kcoil grafting was achieved via thiol coupling, using a unique Kcoil with a terminal cysteine residue. However, cysteine-terminated Kcoil peptides are hard to produce, purify, and oxidize during storage. Indeed, they tend to homodimerize and form disulfide bonds via oxidation of their terminal thiol group, making it impossible to later graft them on thiol-reactive surfaces. Kcoil peptides also contain multiple free amine groups, available for covalent coupling through carbodiimide chemistry. Grafting Kcoil peptides on surfaces via amine coupling would thus guarantee their immobilization regardless of their terminal cysteine's oxidation state, at the expense of the control over their orientation. In this work, we compare Kcoil grafting strategies for the subsequent capture of Ecoil-tagged proteins, for applications such as surface plasmon resonance (SPR) biosensing and cell culture onto protein-decorated substrates. We compare the "classic" thiol coupling of cysteine-terminated Kcoil peptides to the amine coupling of (i) monomeric Kcoil and (ii) dimeric Kcoil-Kcoil linked by a disulfide bond. We have observed that SPR biosensing performances relying on captured Ecoil-tagged proteins were similar for amine-coupled dimeric Kcoil-Kcoil and thiol-coupled Kcoil peptides, at the expense of higher Ecoil-tagged protein consumption. For cell culture applications, Ecoil-tagged growth factors captured on amine-coupled monomeric Kcoil signaled through cell receptors similarly to those captured on thiol-coupled Kcoil peptides. Altogether, while oriented thiol coupling of cysteine-terminated Kcoil peptides remains the most reliable and versatile platform for Ecoil-tagged protein capture, amine coupling of Kcoil peptides, either monomeric or dimerized through a cysteine bond, can offer a good alternative when the challenges and costs associated with the production of monomeric cysteine-tagged Kcoil are too dissuasive for the application.
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Affiliation(s)
- Médéric Dégardin
- Department of Chemical Engineering, Polytechnique Montréal, Montréal H3T 1J4, Québec, Canada
| | - Jimmy Gaudreault
- Department of Chemical Engineering, Polytechnique Montréal, Montréal H3T 1J4, Québec, Canada
| | - Romane Oliverio
- Department of Chemical Engineering, Polytechnique Montréal, Montréal H3T 1J4, Québec, Canada
| | - Benjamin Serafin
- Department of Chemical Engineering, Polytechnique Montréal, Montréal H3T 1J4, Québec, Canada
| | - Catherine Forest-Nault
- Department of Chemical Engineering, Polytechnique Montréal, Montréal H3T 1J4, Québec, Canada
| | - Benoit Liberelle
- Department of Chemical Engineering, Polytechnique Montréal, Montréal H3T 1J4, Québec, Canada
| | - Gregory De Crescenzo
- Department of Chemical Engineering, Polytechnique Montréal, Montréal H3T 1J4, Québec, Canada
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6
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Aliqab K, Sorathiya V, Alsharari M, Dave K, Armghan A. Numerical analysis of hafnium oxide and phase change material-based multi-layered infrared and visible frequency sensor for biomolecules sensing application. Sci Rep 2023; 13:7698. [PMID: 37169783 PMCID: PMC10175553 DOI: 10.1038/s41598-023-34817-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023] Open
Abstract
We report on the results of a numerical investigation into a phase transition material and hafnium (IV) oxide-based refractive index sensor with a wide spectral range, including both the visible and infrared regions of the electromagnetic spectrum. The sensor relies on hafnium (IV) oxide and a phase transition material (HfO2). Three layered versions of the proposed structure are studied; each configuration is built from alternating layers of HfO2, silica, Ge2Sb2Te5(GST), and silver. The three different arrangements have all been studied. The reflectance response of such multilayer structures is discussed in this manuscript for refractive indices ranging from 1 to 2.4. In addition, we have investigated how the varying heights of the materials affect the overall performance of the structure. Finally, we have supplied several formulae for resonating traces that may be used to calculate the sensing behaviour across a specific wavelength range and refractive index values. The corresponding equations are shown below. We have computed numerous equation traces throughout this inquiry to calculate the wavelength and refractive index values. Computational methods may be used to analyze the proposed structure, which might aid in creating biosensors for detecting a wide variety of biomolecules and biomarkers, such as saliva-cortisol, urine, glucose, cancerous and cancerous, and hemoglobin.
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Affiliation(s)
- Khaled Aliqab
- Department of Electrical Engineering, College of Engineering, Jouf University, 72388, Sakaka, Saudi Arabia.
| | - Vishal Sorathiya
- Faculty of Engineering and Technology, Parul Institute of Engineering and Technology, Parul University, Waghodia Road, Vadodara, Gujarat, 391 760, India
| | - Meshari Alsharari
- Department of Electrical Engineering, College of Engineering, Jouf University, 72388, Sakaka, Saudi Arabia
| | - Kavan Dave
- Department of Information and Communication Technology, Marwadi University, Rajkot, India
| | - Ammar Armghan
- Department of Electrical Engineering, College of Engineering, Jouf University, 72388, Sakaka, Saudi Arabia.
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Cao W, Maza JC, Chernyak N, Flygare JA, Krska SW, Toste FD, Francis MB. Modification of Cysteine-Substituted Antibodies Using Enzymatic Oxidative Coupling Reactions. Bioconjug Chem 2023; 34:510-517. [PMID: 36787347 DOI: 10.1021/acs.bioconjchem.2c00576] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Cysteines are routinely used as site-specific handles to synthesize antibody-drug conjugates for targeted immunotherapy applications. Michael additions between thiols and maleimides are some of the most common methods for modifying cysteines, but these functional groups can be difficult to prepare on scale, and the resulting linkages have been shown to be reversible under some physiological conditions. Here, we show that the enzyme tyrosinase, which oxidizes conveniently accessed phenols to afford reactive ortho-quinone intermediates, can be used to attach phenolic cargo to cysteines engineered on antibody surfaces. The resulting linkages between the thiols and ortho-quinones are shown to be more resistant than maleimides to reversion under physiological conditions. Using this approach, we construct antibody conjugates bearing cytotoxic payloads, which exhibit targeted cell killing, and further demonstrate this method for the attachment of a variety of cargo to antibodies, including fluorophores and oligonucleotides.
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Affiliation(s)
- Wendy Cao
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Johnathan C Maza
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Natalia Chernyak
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - John A Flygare
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Shane W Krska
- Department of Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - F Dean Toste
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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8
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Sun B, Xu J, Liu S, Li QX. Characterization of Small Molecule-Protein Interactions Using SPR Method. Methods Mol Biol 2023; 2690:149-159. [PMID: 37450146 DOI: 10.1007/978-1-0716-3327-4_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Surface plasmon resonance (SPR) is an optical phenomenon being used to monitor molecular binding events. With the advantages of being label-free, real-time, and sensitive, SPR assays have become one of the most commonly used techniques to measure binding kinetics, affinity, specificity, and concentration of molecular interactions. In an SPR experiment to measure small molecule-protein interactions, the protein is immobilized on the biosensor surface, while the small molecule flows through the surface of the sensor chip. The interactions between the small molecules and proteins are monitored by subsequent changes in the refractive index and quantified with resonance units. In this chapter, we have utilized an SPR assay to study the interaction of flavonoids and the glucose-regulated protein 78. Assay steps are detailed for immobilization optimization, SPR instrument setup, operation, sample injection, and affinity data analysis.
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Affiliation(s)
- Binmei Sun
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jianmei Xu
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Shaoqun Liu
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA.
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9
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Pospíšil J, Hrabovský M, Bohačiaková D, Hovádková Z, Jurásek M, Mlčoušková J, Paruch K, Nevolová Š, Damborsky J, Hampl A, Jaros J. Geometric Control of Cell Behavior by Biomolecule Nanodistribution. ACS Biomater Sci Eng 2022; 8:4789-4806. [PMID: 36202388 PMCID: PMC9667466 DOI: 10.1021/acsbiomaterials.2c00650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Many dynamic interactions within the cell microenvironment
modulate
cell behavior and cell fate. However, the pathways and mechanisms
behind cell–cell or cell–extracellular matrix interactions
remain understudied, as they occur at a nanoscale level. Recent progress
in nanotechnology allows for mimicking of the microenvironment at
nanoscale in vitro; electron-beam lithography (EBL)
is currently the most promising technique. Although this nanopatterning
technique can generate nanostructures of good quality and resolution,
it has resulted, thus far, in the production of only simple shapes
(e.g., rectangles) over a relatively small area (100 × 100 μm),
leaving its potential in biological applications unfulfilled. Here,
we used EBL for cell-interaction studies by coating cell-culture-relevant
material with electron-conductive indium tin oxide, which formed nanopatterns
of complex nanohexagonal structures over a large area (500 ×
500 μm). We confirmed the potential of EBL for use in cell-interaction
studies by analyzing specific cell responses toward differentially
distributed nanohexagons spaced at 1000, 500, and 250 nm. We found
that our optimized technique of EBL with HaloTags enabled the investigation
of broad changes to a cell-culture-relevant surface and can provide
an understanding of cellular signaling mechanisms at a single-molecule
level.
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Affiliation(s)
- Jakub Pospíšil
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.,Core Facility Cellular Imaging, CEITEC, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Miloš Hrabovský
- TESCAN Orsay Holding a.s., Libušina tř. 863, Brno 623 00, Czech Republic
| | - Dáša Bohačiaková
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.,International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic
| | | | | | - Jarmila Mlčoušková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Kamil Paruch
- International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Šárka Nevolová
- International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic.,Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Jiri Damborsky
- International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic.,Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Aleš Hampl
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.,International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic
| | - Josef Jaros
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.,International Clinical Research Center (ICRC), St. Anne's University Hospital, Pekařská 53, Brno 656 91, Czech Republic
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10
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Liu KH, Liu M, Lin Z, Wang ZF, Chen B, Liu C, Guo A, Konishi M, Yanagisawa S, Wagner G, Sheen J. NIN-like protein 7 transcription factor is a plant nitrate sensor. Science 2022; 377:1419-1425. [PMID: 36137053 DOI: 10.1126/science.add1104] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Nitrate is an essential nutrient and signaling molecule for plant growth. Plants sense intracellular nitrate to adjust their metabolic and growth responses. Here we identify the primary nitrate sensor in plants. We found that mutation of all seven Arabidopsis NIN-like protein (NLP) transcription factors abolished plants' primary nitrate responses and developmental programs. Analyses of NIN-NLP7 chimeras and nitrate binding revealed that NLP7 is derepressed upon nitrate perception via its amino terminus. A genetically encoded fluorescent split biosensor, mCitrine-NLP7, enabled visualization of single-cell nitrate dynamics in planta. The nitrate sensor domain of NLP7 resembles the bacterial nitrate sensor NreA. Substitutions of conserved residues in the ligand-binding pocket impaired the ability of nitrate-triggered NLP7 to control transcription, transport, metabolism, development, and biomass. We propose that NLP7 represents a nitrate sensor in land plants.
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Affiliation(s)
- Kun-Hsiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China.,Institute of Future Agriculture, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China.,Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Menghong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China
| | - Ziwei Lin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Binqing Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China
| | - Cong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China
| | - Aping Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China
| | - Mineko Konishi
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shuichi Yanagisawa
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
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11
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Drozd M, Karoń S, Malinowska E. Recent Advancements in Receptor Layer Engineering for Applications in SPR-Based Immunodiagnostics. SENSORS (BASEL, SWITZERLAND) 2021; 21:3781. [PMID: 34072572 PMCID: PMC8198293 DOI: 10.3390/s21113781] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/23/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022]
Abstract
The rapid progress in the development of surface plasmon resonance-based immunosensing platforms offers wide application possibilities in medical diagnostics as a label-free alternative to enzyme immunoassays. The early diagnosis of diseases or metabolic changes through the detection of biomarkers in body fluids requires methods characterized by a very good sensitivity and selectivity. In the case of the SPR technique, as well as other surface-sensitive detection strategies, the quality of the transducer-immunoreceptor interphase is crucial for maintaining the analytical reliability of an assay. In this work, an overview of general approaches to the design of functional SPR-immunoassays is presented. It covers both immunosensors, the design of which utilizes well-known and often commercially available substrates, as well as the latest solutions developed in-house. Various approaches employing chemical and passive binding, affinity-based antibody immobilization, and the introduction of nanomaterial-based surfaces are discussed. The essence of their influence on the improvement of the main analytical parameters of a given immunosensor is explained. Particular attention is paid to solutions compatible with the latest trends in the development of label-free immunosensors, such as platforms dedicated to real-time monitoring in a quasi-continuous mode, the use of in situ-generated receptor layers (elimination of the regeneration step), and biosensors using recombinant and labelled protein receptors.
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Affiliation(s)
- Marcin Drozd
- Faculty of Chemistry, The Chair of Medical Biotechnology, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
- Center for Advanced Materials and Technologies, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
| | - Sylwia Karoń
- Faculty of Chemistry, The Chair of Medical Biotechnology, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
- Center for Advanced Materials and Technologies, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
| | - Elżbieta Malinowska
- Faculty of Chemistry, The Chair of Medical Biotechnology, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
- Center for Advanced Materials and Technologies, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
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12
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Tunable infrared metamaterial-based biosensor for detection of hemoglobin and urine using phase change material. Sci Rep 2021; 11:7101. [PMID: 33782516 PMCID: PMC8007597 DOI: 10.1038/s41598-021-86700-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 03/09/2021] [Indexed: 02/01/2023] Open
Abstract
This paper reports about the outcomes from an investigation carried out on tunable biosensor for detection using infrared in the range of 1.5 µm and 1.65 µm. The biosensor is made of phase change material formed by different alloy combinations, Ge2Sb2Te5 (GST). The nature of GST allows for the material to change phase with changes in temperature, giving the tunable sensing property for biosensing application. Sensor built with amorphous GST (aGST) and crystalline GST (cGST) in different design structures were tested on different concentrations of biomolecules: hemoglobin (10 g/l, 20 g/l, 30 g/l and 40 g/l); and urine (0-1.5 mg/dL, 2.5 mg/dL, 5 mg/dL and 10 mg/dL). The tunable response observed from the tests demonstrates the potential application of the materials in the design of switching and sensing systems.
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13
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Aktas GB, Ribera A, Skouridou V, Masip L. DNA immobilization and detection using DNA binding proteins. Anal Bioanal Chem 2021; 413:1929-1939. [PMID: 33501551 DOI: 10.1007/s00216-021-03162-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/29/2020] [Accepted: 01/06/2021] [Indexed: 10/22/2022]
Abstract
The immobilization of sensing bioreceptors is a critical feature affecting the final performance of a biosensor. For DNA detection, the (strept)avidin-biotin affinity interaction is often used for the immobilization of biotin-labeled oligonucleotides or PCR amplicons. Herein, DNA binding proteins are proposed as alternative universal anchors for both DNA immobilization and detection, based on the strong and specific affinity interaction between certain DNA binding proteins and their respective dsDNA binding sites. These binding sites can be incorporated in the target DNA molecule during synthesis and by PCR, eliminating the need for post-synthesis chemical modification and resulting in lower costs. When scCro DNA binding protein was immobilized on microplates and nitrocellulose membrane, both ssDNA and dsDNA targets were successfully detected. The detection limits achieved were similar to those obtained with the streptavidin-biotin system. However, the scCro system resulted in higher signals while using less amount of protein. The adsorption properties of scCro were superior to streptavidin's, making scCro a viable alternative as an anchor biomolecule for the development of DNA assays and biosensors. Finally, a nucleic acid lateral flow assay based solely on two different DNA binding proteins, scCro and dHP, was developed for the detection of a PCR amplicon. Overall, the proposed system appears to be very promising and with potential use for multiplex detection using various DNA binding proteins with different sequence specificities. Further work is required to better understand the adsorption properties of these biomolecules on nitrocellulose, optimize the assays comprehensively, and achieve improved sensitivities.
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Affiliation(s)
- Gülsen Betül Aktas
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain
| | - Arnau Ribera
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain
| | - Vasso Skouridou
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain
| | - Lluis Masip
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain.
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14
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Magro M, Venerando A, Macone A, Canettieri G, Agostinelli E, Vianello F. Nanotechnology-Based Strategies to Develop New Anticancer Therapies. Biomolecules 2020; 10:E735. [PMID: 32397196 PMCID: PMC7278173 DOI: 10.3390/biom10050735] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/16/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022] Open
Abstract
The blooming of nanotechnology has made available a limitless landscape of solutions responding to crucial issues in many fields and, nowadays, a wide choice of nanotechnology-based strategies can be adopted to circumvent the limitations of conventional therapies for cancer. Herein, the current stage of nanotechnological applications for cancer management is summarized encompassing the core nanomaterials as well as the available chemical-physical approaches for their surface functionalization and drug ligands as possible therapeutic agents. The use of nanomaterials as vehicles to delivery various therapeutic substances is reported emphasizing advantages, such as the high drug loading, the enhancement of the pay-load half-life and bioavailability. Particular attention was dedicated to highlight the importance of nanomaterial intrinsic features. Indeed, the ability of combining the properties of the transported drug with the ones of the nano-sized carrier can lead to multifunctional theranostic tools. In this view, fluorescence of carbon quantum dots, optical properties of gold nanoparticle and superparamagnetism of iron oxide nanoparticles, are fundamental examples. Furthermore, smart anticancer devices can be developed by conjugating enzymes to nanoparticles, as in the case of bovine serum amine oxidase (BSAO) and gold nanoparticles. The present review is aimed at providing an overall vision on nanotechnological strategies to face the threat of human cancer, comprising opportunities and challenges.
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Affiliation(s)
- Massimiliano Magro
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, 35020 Legnaro (PD), Italy; (M.M.); (A.V.)
| | - Andrea Venerando
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, 35020 Legnaro (PD), Italy; (M.M.); (A.V.)
| | - Alberto Macone
- Department of Biochemical Sciences, A. Rossi Fanelli’, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy;
| | - Gianluca Canettieri
- Pasteur Laboratory, Department of Molecular Medicine, Sapienza University of Rome, I-00161 Rome, Italy;
- International Polyamines Foundation ‘ETS-ONLUS’, Via del Forte Tiburtino 98, 00159 Rome, Italy
| | - Enzo Agostinelli
- Department of Biochemical Sciences, A. Rossi Fanelli’, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy;
- International Polyamines Foundation ‘ETS-ONLUS’, Via del Forte Tiburtino 98, 00159 Rome, Italy
| | - Fabio Vianello
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, 35020 Legnaro (PD), Italy; (M.M.); (A.V.)
- International Polyamines Foundation ‘ETS-ONLUS’, Via del Forte Tiburtino 98, 00159 Rome, Italy
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15
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Sandoval PJ, Santiago J. In Vitro Analytical Approaches to Study Plant Ligand-Receptor Interactions. PLANT PHYSIOLOGY 2020; 182:1697-1712. [PMID: 32034053 PMCID: PMC7140929 DOI: 10.1104/pp.19.01396] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/30/2020] [Indexed: 05/15/2023]
Abstract
State-of-the-art in vitro methods characterize receptor-ligand interactions, highlighting experiment strategies, advantages and limitations.
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Affiliation(s)
- Pedro Jimenez Sandoval
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Julia Santiago
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
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16
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Gorgulla C, Boeszoermenyi A, Wang ZF, Fischer PD, Coote PW, Padmanabha Das KM, Malets YS, Radchenko DS, Moroz YS, Scott DA, Fackeldey K, Hoffmann M, Iavniuk I, Wagner G, Arthanari H. An open-source drug discovery platform enables ultra-large virtual screens. Nature 2020; 580:663-668. [PMID: 32152607 PMCID: PMC8352709 DOI: 10.1038/s41586-020-2117-z] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 02/27/2020] [Indexed: 12/21/2022]
Abstract
On average, an approved drug currently costs US$2-3 billion and takes more than 10 years to develop1. In part, this is due to expensive and time-consuming wet-laboratory experiments, poor initial hit compounds and the high attrition rates in the (pre-)clinical phases. Structure-based virtual screening has the potential to mitigate these problems. With structure-based virtual screening, the quality of the hits improves with the number of compounds screened2. However, despite the fact that large databases of compounds exist, the ability to carry out large-scale structure-based virtual screening on computer clusters in an accessible, efficient and flexible manner has remained difficult. Here we describe VirtualFlow, a highly automated and versatile open-source platform with perfect scaling behaviour that is able to prepare and efficiently screen ultra-large libraries of compounds. VirtualFlow is able to use a variety of the most powerful docking programs. Using VirtualFlow, we prepared one of the largest and freely available ready-to-dock ligand libraries, with more than 1.4 billion commercially available molecules. To demonstrate the power of VirtualFlow, we screened more than 1 billion compounds and identified a set of structurally diverse molecules that bind to KEAP1 with submicromolar affinity. One of the lead inhibitors (iKeap1) engages KEAP1 with nanomolar affinity (dissociation constant (Kd) = 114 nM) and disrupts the interaction between KEAP1 and the transcription factor NRF2. This illustrates the potential of VirtualFlow to access vast regions of the chemical space and identify molecules that bind with high affinity to target proteins.
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Affiliation(s)
- Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA.
- Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Andras Boeszoermenyi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Patrick D Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Paul W Coote
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Krishna M Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yehor S Malets
- Enamine, Kyiv, Ukraine
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
| | - Dmytro S Radchenko
- Enamine, Kyiv, Ukraine
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
| | - Yurii S Moroz
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
- Chemspace, Kyiv, Ukraine
| | - David A Scott
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Konstantin Fackeldey
- Zuse Institute Berlin, Berlin, Germany
- Institute of Mathematics, Technical University Berlin, Berlin, Germany
| | - Moritz Hoffmann
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | | | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
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17
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Maza JC, Ramsey AV, Mehare M, Krska SW, Parish CA, Francis MB. Secondary modification of oxidatively-modified proline N-termini for the construction of complex bioconjugates. Org Biomol Chem 2020; 18:1881-1885. [PMID: 32100807 DOI: 10.1039/d0ob00211a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A convenient two-step method is reported for the ligation of alkoxyamine- or hydrazine-bearing cargo to proline N-termini. Using this approach, bifunctional proline N-terminal bioconjugates are constructed and proline N-terminal proteins are immobilized.
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Affiliation(s)
- Johnathan C Maza
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Alexandra V Ramsey
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Meire Mehare
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Shane W Krska
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, USA
| | - Craig A Parish
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, USA
| | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, California 94720, USA. and Materials Science Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, USA
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18
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Santamaria S. Chemical Modification of Proteoglycanases with Biotin. Methods Mol Biol 2020; 2043:113-123. [PMID: 31463907 DOI: 10.1007/978-1-4939-9698-8_10] [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: 06/10/2023]
Abstract
Biotinylation is a versatile technique that has been used to label proteins for a variety of applications. Under alkaline conditions, the N-hydroxylsuccinimide (NHS) ester present on the biotinylation reagent reacts with primary amines such as the side chain of lysine residues or the N-termini of proteins to yield stable amide bonds. However, the effect of biotinylation on enzyme structure and function has not been generally appreciated. In this chapter, I describe specific issues involving biotinylation of proteoglycanases (e.g., ADAMTS-1, -4, and -5). Taking ADAMTS-5 as an example, I show how high incorporation of biotin molecules causes a decrease in aggrecanase activity, most likely by disrupting exosites present in the cysteine-rich and spacer domains. Such an effect is not evident when enzymatic activity is measured with synthetic peptides, since exosites are not strictly required for peptidolytic activity. Therefore, extreme care must be taken when labeling proteoglycanases and the appropriate enzyme/biotin ratio must be determined experimentally for each enzyme.
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19
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Schroer AB, Mohamed JS, Willard MD, Setola V, Oestreich E, Siderovski DP. A role for Regulator of G protein Signaling-12 (RGS12) in the balance between myoblast proliferation and differentiation. PLoS One 2019; 14:e0216167. [PMID: 31408461 PMCID: PMC6691989 DOI: 10.1371/journal.pone.0216167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/15/2019] [Indexed: 12/28/2022] Open
Abstract
Regulators of G Protein Signaling (RGS proteins) inhibit G protein-coupled receptor (GPCR) signaling by accelerating the GTP hydrolysis rate of activated Gα subunits. Some RGS proteins exert additional signal modulatory functions, and RGS12 is one such protein, with five additional, functional domains: a PDZ domain, a phosphotyrosine-binding domain, two Ras-binding domains, and a Gα·GDP-binding GoLoco motif. RGS12 expression is temporospatially regulated in developing mouse embryos, with notable expression in somites and developing skeletal muscle. We therefore examined whether RGS12 is involved in the skeletal muscle myogenic program. In the adult mouse, RGS12 is expressed in the tibialis anterior (TA) muscle, and its expression is increased early after cardiotoxin-induced injury, suggesting a role in muscle regeneration. Consistent with a potential role in coordinating myogenic signals, RGS12 is also expressed in primary myoblasts; as these cells undergo differentiation and fusion into myotubes, RGS12 protein abundance is reduced. Myoblasts isolated from mice lacking Rgs12 expression have an impaired ability to differentiate into myotubes ex vivo, suggesting that RGS12 may play a role as a modulator/switch for differentiation. We also assessed the muscle regenerative capacity of mice conditionally deficient in skeletal muscle Rgs12 expression (via Pax7-driven Cre recombinase expression), following cardiotoxin-induced damage to the TA muscle. Eight days post-damage, mice lacking RGS12 in skeletal muscle had attenuated repair of muscle fibers. However, when mice lacking skeletal muscle expression of Rgs12 were cross-bred with mdx mice (a model of human Duchenne muscular dystrophy), no increase in muscle degeneration was observed over time. These data support the hypothesis that RGS12 plays a role in coordinating signals during the myogenic program in select circumstances, but loss of the protein may be compensated for within model syndromes of prolonged bouts of muscle damage and repair.
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Affiliation(s)
- Adam B. Schroer
- Department of Physiology & Pharmacology, WVU School of Medicine, West Virginia University, Morgantown, WV, United States of America
| | - Junaith S. Mohamed
- Division of Exercise Physiology, West Virginia University, Morgantown, WV, United States of America
| | - Melinda D. Willard
- Department of Pharmacology, The University of North Carolina, Chapel Hill, NC, United States of America
| | - Vincent Setola
- Department of Neuroscience, West Virginia University, Morgantown, WV, United States of America
| | - Emily Oestreich
- Department of Pharmacology, The University of North Carolina, Chapel Hill, NC, United States of America
- * E-mail: (EO); (DPS)
| | - David P. Siderovski
- Department of Physiology & Pharmacology, WVU School of Medicine, West Virginia University, Morgantown, WV, United States of America
- * E-mail: (EO); (DPS)
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20
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Bräuer M, Zich MT, Önder K, Müller N. The influence of commonly used tags on structural propensities and internal dynamics of peptides. MONATSHEFTE FUR CHEMIE 2019. [DOI: 10.1007/s00706-019-02401-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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21
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Maza JC, Bader DLV, Xiao L, Marmelstein AM, Brauer DD, ElSohly AM, Smith MJ, Krska SW, Parish CA, Francis MB. Enzymatic Modification of N-Terminal Proline Residues Using Phenol Derivatives. J Am Chem Soc 2019; 141:3885-3892. [DOI: 10.1021/jacs.8b10845] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Johnathan C. Maza
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Daniel L. V. Bader
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Lifeng Xiao
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Alan M. Marmelstein
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Daniel D. Brauer
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Adel M. ElSohly
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew J. Smith
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Shane W. Krska
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Craig A. Parish
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Matthew B. Francis
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
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22
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Functional expression of monomeric streptavidin and fusion proteins in Escherichia coli: applications in flow cytometry and ELISA. Appl Microbiol Biotechnol 2018; 102:10079-10089. [PMID: 30250978 DOI: 10.1007/s00253-018-9377-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 02/06/2023]
Abstract
Monomeric streptavidin (mSA) offers a combination of structural and binding properties that are useful in many applications, including a small size and monovalent biotin binding. Because mSA contains a structurally important disulfide bond, the molecule does not fold correctly when expressed inside the cell. We show that mSA can be expressed in a functional form in Escherichia coli by fusing the OmpA signal sequence at the amino terminus. Expressed mSA is exported to the periplasm, from which the molecule leaks to the medium under vigorous shaking. Purified mSA can be conjugated with FITC and used to label microbeads and yeast cells for analysis by flow cytometry, further expanding the scope of mSA-based applications. Some applications require recombinant fusion of mSA with another protein. mSA fused to EGFP cannot be secreted to the medium but was successfully expressed in an engineered cell line that supports oxidative folding in the cytoplasm. Purified mSA-EGFP and mSA-mCherry bound biotin with high affinity and were successfully used in conventional flow cytometry and imaging flow cytometry. Finally, we demonstrate the use of mSA in ELISA, in which horseradish peroxidase-conjugated mSA and biotinylated secondary antibody are used together to detect primary antibody captured on an ELISA plate. Engineering mSA to introduce additional lysine residues can increase the reporter signal above that of wild-type streptavidin. Together, these examples establish mSA as a convenient reagent with a potentially unique role in biotechnology.
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Engineered nanomaterials and human health: Part 1. Preparation, functionalization and characterization (IUPAC Technical Report). PURE APPL CHEM 2018. [DOI: 10.1515/pac-2017-0101] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Abstract
Nanotechnology is a rapidly evolving field, as evidenced by the large number of publications on the synthesis, characterization, and biological/environmental effects of new nano-sized materials. The unique, size-dependent properties of nanomaterials have been exploited in a diverse range of applications and in many examples of nano-enabled consumer products. In this account we focus on Engineered Nanomaterials (ENM), a class of deliberately designed and constructed nano-sized materials. Due to the large volume of publications, we separated the preparation and characterisation of ENM from applications and toxicity into two interconnected documents. Part 1 summarizes nanomaterial terminology and provides an overview of the best practices for their preparation, surface functionalization, and analytical characterization. Part 2 (this issue, Pure Appl. Chem. 2018; 90(8): 1325–1356) focuses on ENM that are used in products that are expected to come in close contact with consumers. It reviews nanomaterials used in therapeutics, diagnostics, and consumer goods and summarizes current nanotoxicology challenges and the current state of nanomaterial regulation, providing insight on the growing public debate on whether the environmental and social costs of nanotechnology outweigh its potential benefits.
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Lago S, Nadai M, Rossetto M, Richter SN. Surface Plasmon Resonance kinetic analysis of the interaction between G-quadruplex nucleic acids and an anti-G-quadruplex monoclonal antibody. Biochim Biophys Acta Gen Subj 2018. [PMID: 29524541 PMCID: PMC5988565 DOI: 10.1016/j.bbagen.2018.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND G-quadruplexes (G4s) are nucleic acids secondary structures formed in guanine-rich sequences. Anti-G4 antibodies represent a tool for the direct investigation of G4s in cells. Surface Plasmon Resonance (SPR) is a highly sensitive technology, suitable for assessing the affinity between biomolecules. We here aimed at improving the orientation of an anti-G4 antibody on the SPR sensor chip to optimize detection of binding antigens. METHODS SPR was employed to characterize the anti-G4 antibody interaction with G4 and non-G4 oligonucleotides. Dextran-functionalized sensor chips were used both in covalent coupling and capturing procedures. RESULTS The use of two leading molecule for orienting the antibody of interest allowed to improve its activity from completely non-functional to 65% active. The specificity of the anti-G4 antobody for G4 structures could thus be assessed with high sensitivity and reliability. CONCLUSIONS Optimization of the immobilization protocol for SPR biosensing, allowed us to determine the anti-G4 antibody affinity and specificity for G4 antigens with higher sensitivity with respect to other in vitro assays such as ELISA. Anti-G4 antibody specificity is a fundamental assumption for the future utilization of this kind of antibodies for monitoring G4s directly in cells. GENERAL SIGNIFICANCE The heterogeneous orientation of amine-coupling immobilized ligands is a general problem that often leads to partial or complete inactivation of the molecules. Here we describe a new strategy for improving ligand orientation: driving it from two sides. This principle can be virtually applied to every molecule that loses its activity or is poorly immobilized after standard coupling to the SPR chip surface.
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Affiliation(s)
- Sara Lago
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Monica Rossetto
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy.
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Fraas R, Diehm J, Franzreb M. Automated Solid-Phase Protein Modification with Integrated Enzymatic Digest for Reaction Validation: Application of a Compartmented Microfluidic Reactor for Rapid Optimization and Analysis of Protein Biotinylation. Front Bioeng Biotechnol 2017; 5:72. [PMID: 29181376 PMCID: PMC5693853 DOI: 10.3389/fbioe.2017.00072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 10/31/2017] [Indexed: 11/13/2022] Open
Abstract
Protein modification by covalent coupling of small ligands or markers is an important prerequisite for the use of proteins in many applications. Well-known examples are the use of proteins with fluorescent markers in many in vivo experiments or the binding of biotinylated antibodies via biotin-streptavidin coupling in the frame of numerous bioassays. Multiple protocols were established for the coupling of the respective molecules, e.g., via the C and N-terminus, or via cysteines and lysines exposed at the protein surface. Still, in most cases the conditions of these standard protocols are only an initial guess. Optimization of the coupling parameters like reagent concentrations, pH, or temperature may strongly increase coupling yield and the biological activity of the modified protein. In order to facilitate the process of optimizing coupling conditions, a method was developed which uses a compartmented microfluidic reactor for the rapid screening of different coupling conditions. In addition, the system allows for the integration of an enzymatic digest of the modified protein directly after modification. In combination with a subsequent MALDI-TOF analysis of the resulting fragments, this gives a fast and detailed picture not only of the number and extent of the generated modifications but also of their position within the protein sequence. The described process was demonstrated for biotinylation of green fluorescent protein. Different biotin-excesses and different pH-values were tested in order to elucidate the influence on the modification extent and pattern. In addition, the results of solid-phase based modifications within the microfluidic reactor were compared to modification patterns resulting from coupling trials with unbound protein. As expected, modification patterns of immobilized proteins showed clear differences to the ones of dissolved proteins.
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Affiliation(s)
- Regina Fraas
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Juliane Diehm
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Matthias Franzreb
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Palla KS, Hurlburt TJ, Buyanin AM, Somorjai GA, Francis MB. Site-Selective Oxidative Coupling Reactions for the Attachment of Enzymes to Glass Surfaces through DNA-Directed Immobilization. J Am Chem Soc 2017; 139:1967-1974. [DOI: 10.1021/jacs.6b11716] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kanwal S. Palla
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States,
| | - Tyler J. Hurlburt
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States,
- Chemical
Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720-1460, United States, and
| | - Alexander M. Buyanin
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States,
- Materials
Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720-1460, United States
| | - Gabor A. Somorjai
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States,
- Chemical
Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720-1460, United States, and
- Materials
Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720-1460, United States
| | - Matthew B. Francis
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States,
- Materials
Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720-1460, United States
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Abstract
Surface plasmon resonance (SPR) is one of the most commonly used techniques to study protein-protein interactions. The main advantage of SPR is it gives on the ability to measure the binding affinities and association/dissociation kinetics of complexes in real time, in a label-free environment, and using relatively small quantities of materials. The method is based on the immobilization of one of the binding partners, called the ligand, on a dedicated sensor surface. Immobilization is followed by the injection of the other partner, called the analyte, over the surface containing the ligand. The binding is monitored by subsequent changes in the refractive index of the medium close to the sensor surface upon injection of the analyte. During the last 10 years, SPR has been intensively used in the study of secretion systems because of its ability to detect highly dynamic complexes that are difficult to investigate using other techniques. This chapter will guide users in the setup of SPR experiments in order to identify protein complexes and to assess their binding affinity or kinetics. It will include detailed protocols for (i) the immobilization of proteins with the amine coupling capture method, (ii) analyte-binding analysis, (iii) affinity/kinetic measurements, and (iv) data analysis.Secretion systems are multiprotein complexes allowing the transport of a large number of effectors from the inside to the outside of bacterial cells. The assembly of these supramolecular machineries is ensured by the formation of protein complexes with extremely different times of stability, from transitory to stable interactions. To understand the function of these machineries as well as their modes of association, it is important to study their building blocks by identifying the different interacting partners and assessing their relative affinities and association/dissociation kinetics. For that purpose, scientists combine genetic, biochemical, and biophysical tools. During the last decade, the use of surface plasmon resonance (SPR) in the study of secretion systems has increased spectacularly [1-12]. This in vitro approach is the method of choice to study such dynamic systems owing to its ability to detect both weak and strong interactions ranging from the millimolar to the nanomolar range [13, 14]. SPR can be used as a primary tool to screen interacting partners or as a validation tool for interactions previously identified by other methods (e.g., bacterial two-hybrid, co-immunoprecipitation, chemical crosslinking). The determination of the affinity or kinetics of an interaction, as can be done by SPR, is fundamental to understanding the nature of binding at the cellular level.
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Affiliation(s)
- Badreddine Douzi
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM), Aix-Marseille Université-Centre National de la Recherche Scientifique (CNRS), 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.
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Prinz F, Puetter V, Holton SJ, Andres D, Stegmann CM, Kwiatkowski D, Prechtl S, Petersen K, Beckmann G, Kreft B, Mumberg D, Fernández-Montalván A. Functional and Structural Characterization of Bub3·BubR1 Interactions Required for Spindle Assembly Checkpoint Signaling in Human Cells. J Biol Chem 2016; 291:11252-67. [PMID: 27030009 DOI: 10.1074/jbc.m115.702142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Indexed: 02/02/2023] Open
Abstract
The spindle assembly checkpoint (SAC) is an essential safeguarding mechanism devised to ensure equal chromosome distribution in daughter cells upon mitosis. The proteins Bub3 and BubR1 are key components of the mitotic checkpoint complex, an essential part of the molecular machinery on which the SAC relies. In the present work we have performed a detailed functional and biochemical characterization of the interaction between human Bub3 and BubR1 in cells and in vitro Our results demonstrate that genetic knockdown of Bub3 abrogates the SAC, promotes apoptosis, and inhibits the proliferation of human cancer cells. We also show that the integrity of the human mitotic checkpoint complex depends on the specific recognition between BubR1 and Bub3, for which the BubR1 Gle2 binding sequence motif is essential. This 1:1 binding event is high affinity, enthalpy-driven and with slow dissociation kinetics. The affinity, kinetics, and thermodynamic parameters of the interaction are differentially modulated by small regions in the N and C termini of the Gle2 binding domain sequence, suggesting the existence of "hotspots" for this protein-protein interaction. Furthermore, we show that specific disruption of endogenous BubR1·Bub3 complexes in human cancer cells phenocopies the effects observed in gene targeting experiments. Our work enhances the current understanding of key members of the SAC and paves the road for the pursuit of novel targeted cancer therapies based on SAC inhibition.
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Affiliation(s)
- Florian Prinz
- TRG Oncology, Bayer Pharma AG, Global Drug Discovery, 13353 Berlin, Germany
| | | | | | | | | | | | | | - Kirstin Petersen
- TRG Oncology, Bayer Pharma AG, Global Drug Discovery, 13353 Berlin, Germany
| | | | - Bertolt Kreft
- TRG Oncology, Bayer Pharma AG, Global Drug Discovery, 13353 Berlin, Germany
| | - Dominik Mumberg
- TRG Oncology, Bayer Pharma AG, Global Drug Discovery, 13353 Berlin, Germany
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Xolalpa W, Rodriguez MS, England P. Real-Time Surface Plasmon Resonance (SPR) for the Analysis of Interactions Between SUMO Traps and Mono- or PolySUMO Moieties. Methods Mol Biol 2016; 1475:99-107. [PMID: 27631800 DOI: 10.1007/978-1-4939-6358-4_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Isolating endogenous SUMOylated proteins is a challenging task due to the high reversibility of this posttranslational modification. We have shown that SUMO traps are useful tools for the enrichment and isolation of proteins modified by SUMO in vitro and in vivo. To characterize the affinity and specificity of different SUMO chains for these traps, that are based on SUMO-interacting motifs, we have used real-time surface plasmon resonance (SPR), which allows a label-free analysis of protein/protein interactions. Here, a protocol to determine the affinities of multivalent SUMO traps for polySUMO chains or mono-SUMO molecules by SPR is presented.
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Affiliation(s)
- Wendy Xolalpa
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, 62100, Cuernavaca, Morelos, Mexico
| | | | - Patrick England
- Plate-forme de Biophysique des Macromolécules et de leurs Interactions, Institut Pasteur, 75724, Paris, France.
- CNRS-UMR 3528, 75724, Paris, France.
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Panchapakesan SSS, Jeng SCY, Unrau PJ. RNA complex purification using high-affinity fluorescent RNA aptamer tags. Ann N Y Acad Sci 2015; 1341:149-55. [PMID: 25585661 DOI: 10.1111/nyas.12663] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
RNA plays important roles in cellular processes, but RNA-protein complexes are notoriously hard to isolate and study. We compare and contrast existing RNA- and protein-purification strategies with the potential of new RNA-tagging systems such as RNA Spinach and RNA Mango. Each RNA aptamer binds a small fluorophore, resulting in a highly fluorescent complex that is thousands of times brighter than the unbound fluorophore. Provided that the aptamer binding affinity is high enough, derivatized dyes can be used in conjunction with these aptamers to purify RNA complexes while simultaneously using their intrinsic fluorescence to track the complex of interest. The known strengths and weakness of these RNA tagging systems are discussed.
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31
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Leder L. Site-specific protein labeling in the pharmaceutical industry: experiences from novartis drug discovery. Methods Mol Biol 2015; 1266:7-27. [PMID: 25560065 DOI: 10.1007/978-1-4939-2272-7_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chemically modified proteins play an important role in several fields of pharmaceutical R&D, starting from various activities in drug discovery all the way down to biopharmaceuticals with improved properties such as antibody-drug conjugates. In the first part of the present chapter the significance and use of labeled proteins in biophysical methods, biochemical and cellular assays, in vivo imaging, and biopharmaceuticals is reviewed in general. In this context, the most relevant methods for site-specific modification of proteins and their application are also described. In the second part of the chapter, in-house (Novartis) results and experience with different techniques for selective protein labeling are discussed, with a focus on chemical or enzymatic (Avi-tag) biotinylation of proteins and their application in biophysical and biochemical assays. It can be concluded that while modern methods of site-specific protein labeling offer new possibilities for pharmaceutical R&D, classical methods are still the mainstay mainly due to being well established. However, site-specific protein labeling is expected to increase in importance, in particular for antibody-drug conjugates and other chemically modified biopharmaceuticals.
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Affiliation(s)
- Lukas Leder
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Novartis Campus, 4056, Basel, Switzerland,
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32
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McCormick AM, Jarmusik NA, Endrizzi EJ, Leipzig ND. Expression, isolation, and purification of soluble and insoluble biotinylated proteins for nerve tissue regeneration. J Vis Exp 2014:e51295. [PMID: 24513608 PMCID: PMC4089494 DOI: 10.3791/51295] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Recombinant protein engineering has utilized Escherichia coli (E. coli) expression systems for nearly 4 decades, and today E. coli is still the most widely used host organism. The flexibility of the system allows for the addition of moieties such as a biotin tag (for streptavidin interactions) and larger functional proteins like green fluorescent protein or cherry red protein. Also, the integration of unnatural amino acids like metal ion chelators, uniquely reactive functional groups, spectroscopic probes, and molecules imparting post-translational modifications has enabled better manipulation of protein properties and functionalities. As a result this technique creates customizable fusion proteins that offer significant utility for various fields of research. More specifically, the biotinylatable protein sequence has been incorporated into many target proteins because of the high affinity interaction between biotin with avidin and streptavidin. This addition has aided in enhancing detection and purification of tagged proteins as well as opening the way for secondary applications such as cell sorting. Thus, biotin-labeled molecules show an increasing and widespread influence in bioindustrial and biomedical fields. For the purpose of our research we have engineered recombinant biotinylated fusion proteins containing nerve growth factor (NGF) and semaphorin3A (Sema3A) functional regions. We have reported previously how these biotinylated fusion proteins, along with other active protein sequences, can be tethered to biomaterials for tissue engineering and regenerative purposes. This protocol outlines the basics of engineering biotinylatable proteins at the milligram scale, utilizing a T7 lac inducible vector and E. coli expression hosts, starting from transformation to scale-up and purification.
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Homaei AA, Sariri R, Vianello F, Stevanato R. Enzyme immobilization: an update. J Chem Biol 2013; 6:185-205. [PMID: 24432134 DOI: 10.1007/s12154-013-0102-9] [Citation(s) in RCA: 479] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 07/31/2013] [Indexed: 11/25/2022] Open
Abstract
Compared to free enzymes in solution, immobilized enzymes are more robust and more resistant to environmental changes. More importantly, the heterogeneity of the immo-bilized enzyme systems allows an easy recovery of both enzymes and products, multiple re-use of enzymes, continuous operation of enzymatic processes, rapid termination of reactions, and greater variety of bioreactor designs. This paper is a review of the recent literatures on enzyme immobilization by various techniques, the need for immobilization and different applications in industry, covering the last two decades. The most recent papers, patents, and reviews on immobilization strategies and application are reviewed.
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Affiliation(s)
- Ahmad Abolpour Homaei
- Department of Biology, Faculty of Science, University of Hormozgan, Bandarabbas, Iran
| | - Reyhaneh Sariri
- Reyhaneh Sariri, Department of Microbiology, Lahijan Branch, Islamic Azad University, Lahijan, Iran
| | - Fabio Vianello
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua, Italy
| | - Roberto Stevanato
- Department of Molecular Sciences and Nanosystems, University of Venice, Venice, Italy
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Totland C, Ying M, Haugen M, Mazengia K, Storstein A, Aarseth J, Martinez A, Vedeler C. Avidity of onconeural antibodies is of clinical relevance. Cancer Immunol Immunother 2013; 62:1393-6. [PMID: 23733227 PMCID: PMC11028593 DOI: 10.1007/s00262-013-1442-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
Onconeural antibodies are important in the detection of paraneoplastic neurological syndromes (PNS). The avidity of Hu, Yo, and CRMP5 antibodies from 100 patients was determined by immunoprecipitation (IP), and 13 of the Yo positive sera were also tested by surface plasmon resonance (SPR). There was a significant association between the results from IP and SPR. Yo antibodies had higher avidity than Hu and CRMP5 antibodies, and both high- and low-avidity antibodies were associated with tumors and PNS. High-avidity Yo antibodies were mainly associated with ovarian cancer, whereas high-avidity Hu and CRMP5 antibodies were mainly associated with small-cell lung cancer. Low-avidity CRMP5 and Yo antibodies were less often detected by a commercial line blot than high-avidity antibodies. The failure to detect low-avidity onconeural antibodies may result in under diagnosis of PNS.
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Affiliation(s)
- Cecilie Totland
- Department of Neurology, Haukeland University Hospital, Jonas Lies vei 65, 5021, Bergen, Norway.
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Trilling AK, Harmsen MM, Ruigrok VJ, Zuilhof H, Beekwilder J. The effect of uniform capture molecule orientation on biosensor sensitivity: Dependence on analyte properties. Biosens Bioelectron 2013; 40:219-26. [DOI: 10.1016/j.bios.2012.07.027] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 06/28/2012] [Accepted: 07/13/2012] [Indexed: 01/25/2023]
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Bosch DE, Kimple AJ, Manning AJ, Muller RE, Willard FS, Machius M, Rogers SL, Siderovski DP. Structural determinants of RGS-RhoGEF signaling critical to Entamoeba histolytica pathogenesis. Structure 2012; 21:65-75. [PMID: 23260656 DOI: 10.1016/j.str.2012.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 11/20/2012] [Accepted: 11/20/2012] [Indexed: 10/27/2022]
Abstract
G protein signaling pathways, as key components of physiologic responsiveness and timing, are frequent targets for pharmacologic intervention. Here, we identify an effector for heterotrimeric G protein α subunit (EhGα1) signaling from Entamoeba histolytica, the causative agent of amoebic colitis. EhGα1 interacts with this effector and guanosine triphosphatase-accelerating protein, EhRGS-RhoGEF, in a nucleotide state-selective fashion. Coexpression of EhRGS-RhoGEF with constitutively active EhGα1 and EhRacC leads to Rac-dependent spreading in Drosophila S2 cells. EhRGS-RhoGEF overexpression in E. histolytica trophozoites leads to reduced migration toward serum and lower cysteine protease activity, as well as reduced attachment to, and killing of, host cells. A 2.3 Å crystal structure of the full-length EhRGS-RhoGEF reveals a putative inhibitory helix engaging the Dbl homology domain Rho-binding surface and the pleckstrin homology domain. Mutational analysis of the EhGα1/EhRGS-RhoGEF interface confirms a canonical "regulator of G protein signaling" domain rather than a RhoGEF-RGS ("rgRGS") domain, suggesting a convergent evolution toward heterotrimeric and small G protein cross-talk.
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Affiliation(s)
- Dustin E Bosch
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adam J Kimple
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alyssa J Manning
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robin E Muller
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Francis S Willard
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mischa Machius
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephen L Rogers
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David P Siderovski
- Department of Physiology and Pharmacology, West Virginia University School of Medicine, Robert C. Byrd Health Sciences Center, Morgantown, WV 26506, USA.
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Cohen SP, Buckley BK, Kosloff M, Garland AL, Bosch DE, Cheng G, Radhakrishna H, Brown MD, Willard FS, Arshavsky VY, Tarran R, Siderovski DP, Kimple AJ. Regulator of G-protein signaling-21 (RGS21) is an inhibitor of bitter gustatory signaling found in lingual and airway epithelia. J Biol Chem 2012; 287:41706-19. [PMID: 23095746 DOI: 10.1074/jbc.m112.423806] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The gustatory system detects tastants and transmits signals to the brain regarding ingested substances and nutrients. Although tastant receptors and taste signaling pathways have been identified, little is known about their regulation. Because bitter, sweet, and umami taste receptors are G protein-coupled receptors (GPCRs), we hypothesized that regulators of G protein signaling (RGS) proteins may be involved. The recent cloning of RGS21 from taste bud cells has implicated this protein in the regulation of taste signaling; however, the exact role of RGS21 has not been precisely defined. Here, we sought to determine the role of RGS21 in tastant responsiveness. Biochemical analyses confirmed in silico predictions that RGS21 acts as a GTPase-accelerating protein (GAP) for multiple G protein α subunits, including adenylyl cyclase-inhibitory (Gα(i)) subunits and those thought to be involved in tastant signal transduction. Using a combination of in situ hybridization, RT-PCR, immunohistochemistry, and immunofluorescence, we demonstrate that RGS21 is not only endogenously expressed in mouse taste buds but also in lung airway epithelial cells, which have previously been shown to express components of the taste signaling cascade. Furthermore, as shown by reverse transcription-PCR, the immortalized human airway cell line 16HBE was found to express transcripts for tastant receptors, RGS21, and downstream taste signaling components. Over- and underexpression of RGS21 in 16HBE cells confirmed that RGS21 acts to oppose bitter tastant signaling to cAMP and calcium second messenger changes. Our data collectively suggests that RGS21 modulates bitter taste signal transduction.
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Affiliation(s)
- Staci P Cohen
- Department of Pharmacology, University of North Carolina Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina 27599-7365, USA
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Tassa C, Liong M, Hilderbrand S, Sandler JE, Reiner T, Keliher EJ, Weissleder R, Shaw SY. On-chip bioorthogonal chemistry enables immobilization of in situ modified nanoparticles and small molecules for label-free monitoring of protein binding and reaction kinetics. LAB ON A CHIP 2012; 12:3103-10. [PMID: 22760641 PMCID: PMC3411869 DOI: 10.1039/c2lc40337d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Efficient methods to immobilize small molecules under continuous-flow microfluidic conditions would greatly improve label-free molecular interaction studies using biosensor technology. At present, small-molecule immobilization chemistries require special conditions and in many cases must be performed outside the detector and microfluidic system where real-time monitoring is not possible. Here, we have developed and optimized a method for on-chip bioorthogonal chemistry that enables rapid, reversible immobilization of small molecules with control over orientation and immobilization density, and apply this technique to surface plasmon resonance (SPR) studies. Immobilized small molecules reverse the orientation of canonical SPR interaction studies, and also enable a variety of new SPR applications including on-chip assembly and interaction studies of multicomponent structures, such as functionalized nanoparticles, and measurement of bioorthogonal reaction rates. We use this approach to demonstrate that on-chip assembled functionalized nanoparticles show a preserved ability to interact with their target protein, and to measure rapid bioorthogonal reaction rates with k(2) > 10(3) M(-1) s(-1). This method offers multiple benefits for microfluidic biological applications, including rapid screening of targeted nanoparticles with vastly decreased nanoparticle synthetic requirements, robust immobilization chemistry in the presence of serum, and a continuous flow technique that mimics biologic contexts better than current methods used to measure bioorthogonal reaction kinetics such as NMR or UV-vis spectroscopy (e.g., stopped flow kinetics). Taken together, this approach constitutes a flexible and powerful technique for evaluating a wide variety of reactions and intermolecular interactions for in vitro or in vivo applications.
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Affiliation(s)
- Carlos Tassa
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Monty Liong
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Scott Hilderbrand
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Jason E. Sandler
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Thomas Reiner
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Edmund J. Keliher
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Stanley Y. Shaw
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
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Bosch DE, Willard FS, Ramanujam R, Kimple AJ, Willard MD, Naqvi NI, Siderovski DP. A P-loop mutation in Gα subunits prevents transition to the active state: implications for G-protein signaling in fungal pathogenesis. PLoS Pathog 2012; 8:e1002553. [PMID: 22383884 PMCID: PMC3285607 DOI: 10.1371/journal.ppat.1002553] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/12/2012] [Indexed: 11/26/2022] Open
Abstract
Heterotrimeric G-proteins are molecular switches integral to a panoply of different physiological responses that many organisms make to environmental cues. The switch from inactive to active Gαβγ heterotrimer relies on nucleotide cycling by the Gα subunit: exchange of GTP for GDP activates Gα, whereas its intrinsic enzymatic activity catalyzes GTP hydrolysis to GDP and inorganic phosphate, thereby reverting Gα to its inactive state. In several genetic studies of filamentous fungi, such as the rice blast fungus Magnaporthe oryzae, a G42R mutation in the phosphate-binding loop of Gα subunits is assumed to be GTPase-deficient and thus constitutively active. Here, we demonstrate that Gα(G42R) mutants are not GTPase deficient, but rather incapable of achieving the activated conformation. Two crystal structure models suggest that Arg-42 prevents a typical switch region conformational change upon Gαi1(G42R) binding to GDP·AlF4− or GTP, but rotameric flexibility at this locus allows for unperturbed GTP hydrolysis. Gα(G42R) mutants do not engage the active state-selective peptide KB-1753 nor RGS domains with high affinity, but instead favor interaction with Gβγ and GoLoco motifs in any nucleotide state. The corresponding Gαq(G48R) mutant is not constitutively active in cells and responds poorly to aluminum tetrafluoride activation. Comparative analyses of M. oryzae strains harboring either G42R or GTPase-deficient Q/L mutations in the Gα subunits MagA or MagB illustrate functional differences in environmental cue processing and intracellular signaling outcomes between these two Gα mutants, thus demonstrating the in vivo functional divergence of G42R and activating G-protein mutants. Heterotrimeric G-proteins function as molecular switches to convey cellular signals. When a G-protein coupled receptor encounters its ligand at the cellular membrane, it catalyzes guanine nucleotide exchange on the Gα subunit, resulting in a shift from an inactive to an active conformation. G-protein signaling pathways are conserved from mammals to plants and fungi, including the rice blast fungus Magnaporthe oryzae. A mutation in the Gα subunit (G42R), previously thought to eliminate its GTPase activity, leading to constitutive activation, has been utilized to investigate roles of heterotrimeric G-protein signaling pathways in multiple species of filamentous fungi. Here, we demonstrate through structural, biochemical, and cellular approaches that G42R mutants are neither GTPase deficient nor constitutively active, but rather are unable to transition to the activated conformation. A direct comparison of M. oryzae fungal strains harboring either G42R or truly constitutively activating mutations in two Gα subunits, MagA and MagB, revealed markedly different phenotypes. Our results suggest that activation of MagB is critical for pathogenic development of M. oryzae in response to hydrophobic surfaces, such as plant leaves. Furthermore, the lack of constitutive activity by Gα(G42R) mutants prompts a re-evaluation of its use in previous genetic experiments in multiple fungal species.
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Affiliation(s)
- Dustin E. Bosch
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Francis S. Willard
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (FSW); (DPS)
| | - Ravikrishna Ramanujam
- Fungal Patho-Biology Group, Temasek Life Sciences Laboratory, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Adam J. Kimple
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Melinda D. Willard
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Naweed I. Naqvi
- Fungal Patho-Biology Group, Temasek Life Sciences Laboratory, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - David P. Siderovski
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC Neuroscience Center and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (FSW); (DPS)
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Pro42and Val45of staphylokinase modulate intermolecular interactions of His43-Tyr44pair and specificity of staphylokinase-plasmin activator complex. FEBS Lett 2012; 586:653-8. [DOI: 10.1016/j.febslet.2012.01.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 01/19/2012] [Indexed: 11/21/2022]
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Bosch DE, Kimple AJ, Sammond DW, Muller RE, Miley MJ, Machius M, Kuhlman B, Willard FS, Siderovski DP. Structural determinants of affinity enhancement between GoLoco motifs and G-protein alpha subunit mutants. J Biol Chem 2011; 286:3351-8. [PMID: 21115486 PMCID: PMC3030341 DOI: 10.1074/jbc.m110.190496] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 11/01/2010] [Indexed: 11/06/2022] Open
Abstract
GoLoco motif proteins bind to the inhibitory G(i) subclass of G-protein α subunits and slow the release of bound GDP; this interaction is considered critical to asymmetric cell division and neuro-epithelium and epithelial progenitor differentiation. To provide protein tools for interrogating the precise cellular role(s) of GoLoco motif/Gα(i) complexes, we have employed structure-based protein design strategies to predict gain-of-function mutations that increase GoLoco motif binding affinity. Here, we describe fluorescence polarization and isothermal titration calorimetry measurements showing three predicted Gα(i1) point mutations, E116L, Q147L, and E245L; each increases affinity for multiple GoLoco motifs. A component of this affinity enhancement results from a decreased rate of dissociation between the Gα mutants and GoLoco motifs. For Gα(i1)(Q147L), affinity enhancement was seen to be driven by favorable changes in binding enthalpy, despite reduced contributions from binding entropy. The crystal structure of Gα(i1)(Q147L) bound to the RGS14 GoLoco motif revealed disorder among three peptide residues surrounding a well defined Leu-147 side chain. Monte Carlo simulations of the peptide in this region showed a sampling of multiple backbone conformations in contrast to the wild-type complex. We conclude that mutation of Glu-147 to leucine creates a hydrophobic surface favorably buried upon GoLoco peptide binding, yet the hydrophobic Leu-147 also promotes flexibility among residues 511-513 of the RGS14 GoLoco peptide.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David P. Siderovski
- From the Departments of Pharmacology and
- University of North Carolina Neuroscience Center, and
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
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