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Day K, Schneible JD, Young AT, Pozdin VA, Van Den Driessche G, Gaffney LA, Prodromou R, Freytes DO, Fourches D, Daniele M, Menegatti S. Photoinduced reconfiguration to control the protein-binding affinity of azobenzene-cyclized peptides. J Mater Chem B 2021; 8:7413-7427. [PMID: 32661544 DOI: 10.1039/d0tb01189d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The impact of next-generation biorecognition elements (ligands) will be determined by the ability to remotely control their binding activity for a target biomolecule in complex environments. Compared to conventional mechanisms for regulating binding affinity (pH, ionic strength, or chaotropic agents), light provides higher accuracy and rapidity, and is particularly suited for labile targets. In this study, we demonstrate a general method to develop azobenzene-cyclized peptide ligands with light-controlled affinity for target proteins. Light triggers a cis/trans isomerization of the azobenzene, which results in a major structural rearrangement of the cyclic peptide from a non-binding to a binding configuration. Critical to this goal are the ability to achieve efficient photo-isomerization under low light dosage and the temporal stability of both cis and trans isomers. We demonstrated our method by designing photo-switchable peptides targeting vascular cell adhesion marker 1 (VCAM1), a cell marker implicated in stem cell function. Starting from a known VCAM1-binding linear peptide, an ensemble of azobenzene-cyclized variants with selective light-controlled binding were identified by combining in silico design with experimental characterization via spectroscopy and surface plasmon resonance. Variant cycloAZOB[G-VHAKQHRN-K] featured rapid, light-controlled binding of VCAM1 (KD,trans/KD,cis ∼ 130). Biotin-cycloAZOB[G-VHAKQHRN-K] was utilized to label brain microvascular endothelial cells (BMECs), showing co-localization with anti-VCAM1 antibodies in cis configuration and negligible binding in trans configuration.
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Affiliation(s)
- Kevin Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina, USA.
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Deiber JA, Peirotti MB, Piaggio MV. Charge regulation phenomenon predicted from the modeling of polypeptide electrophoretic mobilities as a relevant mechanism of amyloid-beta peptide oligomerization. Electrophoresis 2016; 37:711-8. [DOI: 10.1002/elps.201500391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/10/2015] [Accepted: 12/16/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Julio A. Deiber
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC), Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe Argentina
| | - Marta B. Peirotti
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC), Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe Argentina
| | - Maria V. Piaggio
- Cátedra de Bioquímica Básica de Macromoléculas, Facultad de Bioquímica y Ciencias Biológicas; UNL; Santa Fe Argentina
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Deiber JA, Peirotti MB, Piaggio MV. Global properties and propensity to dimerization of the amyloid-beta (12-28) peptide fragment through the modeling of its monomer and dimer diffusion coefficients and electrophoretic mobilities. Electrophoresis 2015; 36:805-12. [DOI: 10.1002/elps.201400395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/20/2014] [Accepted: 11/05/2014] [Indexed: 01/20/2023]
Affiliation(s)
- Julio A. Deiber
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe Argentina
| | - Marta B. Peirotti
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe Argentina
| | - Maria V. Piaggio
- Cátedra de Bioquímica Básica de Macromoléculas; Facultad de Bioquímica y Ciencias Biológicas, UNL; Santa Fe Argentina
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Chamieh J, Koval D, Besson A, Kašička V, Cottet H. Generalized polymer effective charge measurement by capillary isotachophoresis. J Chromatogr A 2014; 1370:255-62. [DOI: 10.1016/j.chroma.2014.10.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 10/03/2014] [Accepted: 10/09/2014] [Indexed: 12/22/2022]
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Deiber JA, Piaggio MV, Peirotti MB. Estimation of electrokinetic and hydrodynamic global properties of relevant amyloid-beta peptides through the modeling of their effective electrophoretic mobilities and analysis of their propensities to aggregation. J Sep Sci 2014; 37:2618-24. [DOI: 10.1002/jssc.201400533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 06/11/2014] [Accepted: 06/16/2014] [Indexed: 01/27/2023]
Affiliation(s)
- Julio A. Deiber
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe Argentina
| | - Maria V. Piaggio
- Cátedra de Bioquímica Básica de Macromoléculas; Facultad de Bioquímica y Ciencias Biológicas, UNL; Santa Fe Argentina
| | - Marta B. Peirotti
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe Argentina
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Allison SA, Wu H, Bui TM, Dang L, Huynh GH, Nguyen T, Soegiarto L, Truong BC. Specific ion effects on the electrophoretic mobility of small, highly charged peptides: A modeling study. J Sep Sci 2014; 37:2403-10. [DOI: 10.1002/jssc.201400484] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/09/2014] [Accepted: 06/10/2014] [Indexed: 11/08/2022]
Affiliation(s)
| | - Hengfu Wu
- Department of Chemistry; Georgia State University; Atlanta GA USA
| | - Tuyen M. Bui
- Department of Chemistry; Georgia State University; Atlanta GA USA
| | - Lac Dang
- Department of Chemistry; Georgia State University; Atlanta GA USA
| | - Giang H. Huynh
- Department of Chemistry; Georgia State University; Atlanta GA USA
| | - Tam Nguyen
- Department of Chemistry; Georgia State University; Atlanta GA USA
| | - Linda Soegiarto
- Department of Chemistry; Georgia State University; Atlanta GA USA
| | - Bi C. Truong
- Department of Chemistry; Georgia State University; Atlanta GA USA
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Deiber JA, Piaggio MV, Peirotti MB. Global chain properties of an alll-α-eicosapeptide with a secondary α-helix and its all retrod-inverso-α-eicosapeptide estimated through the modeling of their CZE-determined electrophoretic mobilities. Electrophoresis 2013; 35:755-61. [DOI: 10.1002/elps.201300395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 09/26/2013] [Accepted: 10/11/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Julio A. Deiber
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe Argentina
| | - Maria V. Piaggio
- Cátedra de Bioquímica Básica de Macromoléculas; Facultad de Bioquímica y Ciencias Biológicas; UNL; Santa Fe Argentina
| | - Marta B. Peirotti
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe Argentina
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Deiber JA, Piaggio MV, Peirotti MB. Evaluation of the slip length in the slipping friction between background electrolytes and peptides through the modeling of their capillary zone electrophoretic mobilities. Electrophoresis 2013; 34:2648-54. [DOI: 10.1002/elps.201300102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 03/30/2013] [Accepted: 04/02/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Julio A. Deiber
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); UNL, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
| | - Maria V. Piaggio
- Cátedra de Bioquímica Básica de Macromoléculas; Facultad de Bioquímica y Ciencias Biológicas; Universidad Nacional del Litoral (UNL); Santa Fe; Argentina
| | - Marta B. Peirotti
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); UNL, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
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Deiber JA, Piaggio MV, Peirotti MB. Determination of electrokinetic and hydrodynamic parameters of proteins by modeling their electrophoretic mobilities through the electrically charged spherical soft particle. Electrophoresis 2013; 34:708-15. [DOI: 10.1002/elps.201200463] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/03/2012] [Accepted: 10/17/2012] [Indexed: 01/23/2023]
Affiliation(s)
- Julio A. Deiber
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
| | - María V. Piaggio
- Cátedra de Bioquímica Básica de Macromoléculas; Facultad de Bioquímica y Ciencias Biológicas; UNL; Santa Fe; Argentina
| | - Marta B. Peirotti
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
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Deiber JA, Piaggio MV, Peirotti MB. Determination of electrokinetic and hydrodynamic parameters of proteins by modeling their electrophoretic mobilities through the electrically charged spherical porous particle. Electrophoresis 2013; 34:700-7. [DOI: 10.1002/elps.201200405] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/02/2012] [Accepted: 10/17/2012] [Indexed: 11/12/2022]
Affiliation(s)
- Julio A. Deiber
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
| | - Maria V. Piaggio
- Cátedra de Bioquímica Básica de Macromoléculas; Facultad de Bioquímica y Ciencias Biológicas; UNL; Santa Fe; Argentina
| | - Marta B. Peirotti
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
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Ibrahim A, Ohshima H, Allison SA, Cottet H. Determination of effective charge of small ions, polyelectrolytes and nanoparticles by capillary electrophoresis. J Chromatogr A 2012; 1247:154-64. [PMID: 22683187 DOI: 10.1016/j.chroma.2012.05.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/27/2012] [Accepted: 05/01/2012] [Indexed: 11/28/2022]
Abstract
In this paper, a systematic and comparative study related to the effective charge determination of three kinds of solutes (small ions, polyelectrolytes and nanoparticles) was performed. Four approaches were compared regarding their conditions of validity and their advantages/disadvantages. Three of them allow the effective charge determination from the electrophoretic mobility and the hydrodynamic radius of the solutes using electrophoretic mobility modelings based on Nernst-Einstein (NE), O'Brien-White-Ohshima (OWO) and Yoon and Kim (YK) equations. Electrophoretic mobility and hydrodynamic radius were determined by capillary electrophoresis and Taylor dispersion analysis, respectively, using the same instrumentation in similar conditions, on a large set of samples. A fourth experimental approach based on the sensitivity of detection in indirect UV detection mode (IUV) was compared to the previously mentioned methods. OWO and YK modelings are well adapted for the effective charge determination of small ions and nanoparticles, while IUV is the only method adapted for polyelectrolytes.
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Affiliation(s)
- Amal Ibrahim
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier 1-2, Place Eugène Bataillon CC 1706, 34095 Montpellier Cedex 5, France
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Wernersson E, Heyda J, Kubíčková A, Křížek T, Coufal P, Jungwirth P. Counterion condensation in short cationic peptides: Limiting mobilities beyond the Onsager-Fuoss theory. Electrophoresis 2012; 33:981-9. [DOI: 10.1002/elps.201100602] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Jan Heyda
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems; Prague; Czech Republic
| | - Anna Kubíčková
- Charles University in Prague; Faculty of Science; Department of Analytical Chemistry; Prague; Czech Republic
| | - Tomáš Křížek
- Charles University in Prague; Faculty of Science; Department of Analytical Chemistry; Prague; Czech Republic
| | - Pavel Coufal
- Charles University in Prague; Faculty of Science; Department of Analytical Chemistry; Prague; Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems; Prague; Czech Republic
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Deiber JA, Peirotti MB, Piaggio MV. Interplay between electrophoretic mobility and intrinsic viscosity of polypeptide chains. Electrophoresis 2012; 33:990-9. [DOI: 10.1002/elps.201100637] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Julio A. Deiber
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
| | - Marta B. Peirotti
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
| | - María V. Piaggio
- Cátedra de Bioquímica Básica de Macromoléculas,; Facultad de Bioquímica y Ciencias Biológicas; UNL; Santa Fe; Argentina
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Abstract
CE is used to measure the electrophoretic mobility of low molecular mass oligo-L-lysines (n=1-8) in aqueous LiH₂PO₄ buffer, BGE, at pH 2.5 over a range of temperatures (25-50 °C) and ionic strengths (10-100 mM). Mobilities are corrected for Joule heating and under the conditions of the experiment, interaction of the peptides with the capillary walls can be ignored. A "coarse grained" bead modeling methodology (BMM) (H. Pei et al., J. Chromatogr. A 2009, 1216, 1908-1916) is used to model the mobilities. This model partially accounts for peptide conformation as well as the assumed form of its secondary structure. For highly charged oligolysines, it is necessary to properly account for the relaxation effect. In the present study, the BMM approach tends to overestimate oligolysine mobility and that effect tends to increase with increasing ionic strength and peptide length. It is proposed that association between the oligolysines and buffer components (H₂PO₄⁻ in this case) that go beyond classical electrostatic interactions are responsible for this discrepancy. A simple binding model is introduced that illustrates how this association can reconcile model and experiment.
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Affiliation(s)
- Stuart A Allison
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.
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Deiber JA, Piaggio MV, Peirotti MB. Global conformations of proteins as predicted from the modeling of their CZE mobility data. Electrophoresis 2011; 32:2779-87. [DOI: 10.1002/elps.201100016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 02/07/2011] [Accepted: 02/10/2011] [Indexed: 11/11/2022]
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Allison SA, Pei H, Allen M, Brown J, Kim CI, Zhen Y. Modeling the electrophoresis and transport of peptides: The effective sphere model and complex formation. J Sep Sci 2010; 33:2439-46. [DOI: 10.1002/jssc.201000130] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Piaggio MV, Peirotti MB, Deiber JA. Estimation of global structural and transport properties of peptides through the modeling of their CZE mobility data. J Sep Sci 2010; 33:2423-9. [DOI: 10.1002/jssc.201000134] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Allison SA, Pei H, Baek S, Brown J, Lee MY, Nguyen V, Twahir UT, Wu H. The dependence of the electrophoretic mobility of small organic ions on ionic strength and complex formation. Electrophoresis 2010; 31:920-32. [DOI: 10.1002/elps.200900625] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Piaggio MV, Peirotti MB, Deiber JA. Analysis of the interplay among charge, hydration and shape of proteins through the modeling of their CZE mobility data. Electrophoresis 2009; 30:2328-36. [DOI: 10.1002/elps.200800743] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Jing J, Liang G, Mei H, Xiao S, Xia Z, Li Z. Quantitative structure–mobility relationship studies of dipeptides in capillary zone electrophoresis using three-dimensional holographic vector of atomic interaction field. MOLECULAR SIMULATION 2009. [DOI: 10.1080/08927020802512203] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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The free solution electrophoretic mobility of peptides by a bead modeling methodology. J Chromatogr A 2009; 1216:1908-16. [DOI: 10.1016/j.chroma.2008.09.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 09/02/2008] [Accepted: 09/04/2008] [Indexed: 11/24/2022]
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