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Valencia-Martínez H, Riaño-Umbarila L, Olamendi-Portugal T, Romero-Moreno JA, Possani LD, Becerril B. Neutralization of Centruroides tecomanus scorpion venom by the use of two human recombinant antibody fragments. Mol Immunol 2023; 164:79-87. [PMID: 37980772 DOI: 10.1016/j.molimm.2023.11.001] [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] [Received: 06/06/2023] [Revised: 09/06/2023] [Accepted: 11/02/2023] [Indexed: 11/21/2023]
Abstract
The first toxic component identified against mammals in the venom from Centruroides tecomanus scorpion from Colima, Mexico was Ct1a toxin, which was neutralized by human single chain variable fragment (scFv) RAS27. Venom characterization from these scorpions collected on the Pacific coast of Colima, enabled the identification of a second component of medical importance named Ct71 toxin. Amino acid sequence of Ct71 shares a high identity with Chui5 toxin from C. huichol scorpion, which was neutralized by scFv HV. For this reason, the kinetic parameters of interaction between Ct71 toxin and scFv HV were determined by surface plasmon resonance. Results showed a significantly higher affinity for Ct71 as compared to Chui5. As expected, this toxin was neutralized by scFv HV. The injection of a mixture of scFvs HV and RAS27, resulted in the neutralization of C. tecomanus venom, corroborating that human recombinant antibody fragments can efficiently contribute to the neutralization of medically important toxins and their respective venoms from Mexican scorpions.
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Affiliation(s)
- Hugo Valencia-Martínez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca, 62250, Mexico
| | - Lidia Riaño-Umbarila
- Investigadora por México, CONAHCyT-Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca 62250, Mexico
| | - Timoteo Olamendi-Portugal
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca, 62250, Mexico
| | - José Alberto Romero-Moreno
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca, 62250, Mexico
| | - Lourival D Possani
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca, 62250, Mexico
| | - Baltazar Becerril
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca, 62250, Mexico.
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2
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Abstract
In the computational design of antibodies, the interaction analysis between target antigen and antibody is an essential process to obtain feedback for validation and optimization of the design. Kinetic and thermodynamic parameters as well as binding affinity (KD) allow for a more detailed evaluation and understanding of the molecular recognition. In this chapter, we summarize the conventional experimental methods which can calculate KD value (ELISA, FP), analyze a binding activity to actual cells (FCM), and evaluate the kinetic and thermodynamic parameters (ITC, SPR, BLI), including high-throughput analysis and a recently developed experimental technique.
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Affiliation(s)
- Aki Tanabe
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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3
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Valencia-Martínez H, Olamendi-Portugal T, Restano-Cassulini R, Serrano-Posada H, Zamudio F, Possani LD, Riaño-Umbarila L, Becerril B. Characterization of Four Medically Important Toxins from Centruroides huichol Scorpion Venom and Its Neutralization by a Single Recombinant Antibody Fragment. Toxins (Basel) 2022; 14:toxins14060369. [PMID: 35737030 PMCID: PMC9227038 DOI: 10.3390/toxins14060369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
Centruroides huichol scorpion venom is lethal to mammals. Analysis of the venom allowed the characterization of four lethal toxins named Chui2, Chui3, Chui4, and Chui5. scFv 10FG2 recognized well all toxins except Chui5 toxin, therefore a partial neutralization of the venom was observed. Thus, scFv 10FG2 was subjected to three processes of directed evolution and phage display against Chui5 toxin until obtaining scFv HV. Interaction kinetic constants of these scFvs with the toxins were determined by surface plasmon resonance (SPR) as well as thermodynamic parameters of scFv variants bound to Chui5. In silico models allowed to analyze the molecular interactions that favor the increase in affinity. In a rescue trial, scFv HV protected 100% of the mice injected with three lethal doses 50 (LD50) of venom. Moreover, in mix-type neutralization assays, a combination of scFvs HV and 10FG2 protected 100% of mice injected with 5 LD50 of venom with moderate signs of intoxication. The ability of scFv HV to neutralize different toxins is a significant achievement, considering the diversity of the species of Mexican venomous scorpions, so this scFv is a candidate to be part of a recombinant anti-venom against scorpion stings in Mexico.
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Affiliation(s)
- Hugo Valencia-Martínez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca 62250, Mexico; (H.V.-M.); (T.O.-P.); (R.R.-C.); (F.Z.); (L.D.P.)
| | - Timoteo Olamendi-Portugal
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca 62250, Mexico; (H.V.-M.); (T.O.-P.); (R.R.-C.); (F.Z.); (L.D.P.)
| | - Rita Restano-Cassulini
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca 62250, Mexico; (H.V.-M.); (T.O.-P.); (R.R.-C.); (F.Z.); (L.D.P.)
| | - Hugo Serrano-Posada
- Investigador por México, CONACyT-Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología-Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, Colima 28627, Mexico;
| | - Fernando Zamudio
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca 62250, Mexico; (H.V.-M.); (T.O.-P.); (R.R.-C.); (F.Z.); (L.D.P.)
| | - Lourival D. Possani
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca 62250, Mexico; (H.V.-M.); (T.O.-P.); (R.R.-C.); (F.Z.); (L.D.P.)
| | - Lidia Riaño-Umbarila
- Investigadora por México, CONACyT-Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca 62250, Mexico
- Correspondence: (L.R.-U.); (B.B.); Tel.: +52-(777)-329-1669 (B.B.)
| | - Baltazar Becerril
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca 62250, Mexico; (H.V.-M.); (T.O.-P.); (R.R.-C.); (F.Z.); (L.D.P.)
- Correspondence: (L.R.-U.); (B.B.); Tel.: +52-(777)-329-1669 (B.B.)
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4
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Bucaite G, Kang-Pettinger T, Moreira J, Gould HJ, James LK, Sutton BJ, McDonnell JM. Interplay between Affinity and Valency in Effector Cell Degranulation: A Model System with Polcalcin Allergens and Human Patient-Derived IgE Antibodies. THE JOURNAL OF IMMUNOLOGY 2019; 203:1693-1700. [PMID: 31462504 DOI: 10.4049/jimmunol.1900509] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/19/2019] [Indexed: 01/10/2023]
Abstract
An allergic reaction is rapidly generated when allergens bind and cross-link IgE bound to its receptor FcεRI on effector cells, resulting in cell degranulation and release of proinflammatory mediators. The extent of effector cell activation is linked to allergen affinity, oligomeric state, valency, and spacing of IgE-binding epitopes on the allergen. Whereas most of these observations come from studies using synthetic allergens, in this study we have used Timothy grass pollen allergen Phl p 7 and birch pollen allergen Bet v 4 to study these effects. Despite the high homology of these polcalcin family allergens, Phl p 7 and Bet v 4 display different binding characteristics toward two human patient-derived polcalcin-specific IgE Abs. We have used native polcalcin dimers and engineered multimeric allergens to test the effects of affinity and oligomeric state on IgE binding and effector cell activation. Our results indicate that polcalcin multimers are required to stimulate high levels of effector cell degranulation when using the humanized RBL-SX38 cell model and that multivalency can overcome the need for high-affinity interactions.
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Affiliation(s)
- Gintare Bucaite
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom.,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom
| | - Tara Kang-Pettinger
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom.,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom.,Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and
| | - Jorge Moreira
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom.,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom
| | - Hannah J Gould
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom.,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom
| | - Louisa K James
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom.,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom.,Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, United Kingdom
| | - Brian J Sutton
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom.,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom
| | - James M McDonnell
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom; .,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom
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5
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A large-scale comparative analysis of affinity, thermodynamics and functional characteristics of interactions of twelve cytochrome P450 isoforms and their redox partners. Biochimie 2019; 162:156-166. [DOI: 10.1016/j.biochi.2019.04.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/24/2019] [Indexed: 12/16/2022]
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6
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Thomsen L, Gurevich L. A surface plasmon resonance assay for characterisation and epitope mapping of anti-GLP-1 antibodies. J Mol Recognit 2018; 31:e2711. [PMID: 29671912 DOI: 10.1002/jmr.2711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 01/28/2018] [Accepted: 02/19/2018] [Indexed: 11/07/2022]
Abstract
The incretin hormone glucagon-like peptide-1 (GLP-1) has been subject to substantial pharmaceutical research regarding the treatment of type 2 diabetes mellitus. However, quantification of GLP-1 levels remains complicated due to the low circulation concentration and concurrent existence of numerous metabolites, homologous peptides, and potentially introduced GLP-1 receptor agonists. Surface plasmon resonance (SPR) facilitates real-time monitoring allowing a more detailed characterisation of the interaction compared with conventional enzyme-linked immunosorbent assays (ELISA). In this paper, we describe the development of the first SPR assays for characterisation of anti-GLP-1 antibodies for ELISA purposes. Binding responses were obtained on covalently immobilised anti-GLP-1 antibodies at 12°C, 25°C, and 40°C and fitted to a biomolecular (1:1) interaction model showing association rates of 1.01 × 103 to 4.54 × 103 M-1 s-1 and dissociation rates of 3.56 × 10-5 to 1.56 × 10-3 s-1 leading to affinities of 35.2 to 344 nM, depending on the temperature. Determination of thermodynamic properties revealed an enthalpy driven interaction (ΔH < ΔS < 0) with higher affinities at lower temperatures due to the formation and stabilisation of hydrogen bonds within the binding site primarily composed of polar amino acids (ΔCp < 0). Pair-wise epitope mapping was performed on captured anti-GLP-1 antibodies followed by subsequent interaction with GLP-1 (7-36) and other anti-GLP-1 antibodies. A global evaluation of every binding response led to an epitope map elucidating the potential of various anti-GLP-1 antibody pairs for sandwich ELISA and hence pinpointing the optimal antibody combinations. The SPR assays proved capable of providing vital information for ELISA development endorsing it as a useful optimisation tool.
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Affiliation(s)
- Lasse Thomsen
- Institute of Physics and Nanotechnology, Aalborg University, 9220, Aalborg Ø, Denmark
| | - Leonid Gurevich
- Institute of Physics and Nanotechnology, Aalborg University, 9220, Aalborg Ø, Denmark
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7
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Docking, thermodynamics and molecular dynamics (MD) studies of a non-canonical protease inhibitor, MP-4, from Mucuna pruriens. Sci Rep 2018; 8:689. [PMID: 29330385 PMCID: PMC5766534 DOI: 10.1038/s41598-017-18733-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/15/2017] [Indexed: 11/14/2022] Open
Abstract
Sequence and structural homology suggests that MP-4 protein from Mucuna pruriens belongs to Kunitz-type protease inhibitor family. However, biochemical assays showed that this protein is a poor inhibitor of trypsin. To understand the basis of observed poor inhibition, thermodynamics and molecular dynamics (MD) simulation studies on binding of MP-4 to trypsin were carried out. Molecular dynamics simulations revealed that temperature influences the spectrum of conformations adopted by the loop regions in the MP-4 structure. At an optimal temperature, MP-4 achieves maximal binding while above and below the optimum temperature, its functional activity is hampered due to unfavourable flexibility and relative rigidity, respectively. The low activity at normal temperature is due to the widening of the conformational spectrum of the Reactive Site Loop (RSL) that reduces the probability of formation of stabilizing contacts with trypsin. The unique sequence of the RSL enhances flexibility at ambient temperature and thus reduces its ability to inhibit trypsin. This study shows that temperature influences the function of a protein through modulation in the structure of functional domain of the protein. Modulation of function through appearance of new sequences that are more sensitive to temperature may be a general strategy for evolution of new proteins.
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8
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Deganutti G, Zhukov A, Deflorian F, Federico S, Spalluto G, Cooke RM, Moro S, Mason JS, Bortolato A. Impact of protein-ligand solvation and desolvation on transition state thermodynamic properties of adenosine A 2A ligand binding kinetics. In Silico Pharmacol 2017; 5:16. [PMID: 29308352 PMCID: PMC5755719 DOI: 10.1007/s40203-017-0037-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/14/2017] [Indexed: 12/26/2022] Open
Abstract
Ligand-protein binding kinetic rates are growing in importance as parameters to consider in drug discovery and lead optimization. In this study we analysed using surface plasmon resonance (SPR) the transition state (TS) properties of a set of six adenosine A2A receptor inhibitors, belonging to both the xanthine and the triazolo-triazine scaffolds. SPR highlighted interesting differences among the ligands in the enthalpic and entropic components of the TS energy barriers for the binding and unbinding events. To better understand at a molecular level these differences, we developed suMetaD, a novel molecular dynamics (MD)-based approach combining supervised MD and metadynamics. This method allows simulation of the ligand unbinding and binding events. It also provides the system conformation corresponding to the highest energy barrier the ligand is required to overcome to reach the final state. For the six ligands evaluated in this study their TS thermodynamic properties were linked in particular to the role of water molecules in solvating/desolvating the pocket and the small molecules. suMetaD identified kinetic bottleneck conformations near the bound state position or in the vestibule area. In the first case the barrier is mainly enthalpic, requiring the breaking of strong interactions with the protein. In the vestibule TS location the kinetic bottleneck is instead mainly of entropic nature, linked to the solvent behaviour.
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Affiliation(s)
- Giuseppe Deganutti
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, Padua, Italy
| | - Andrei Zhukov
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Herts AL7 3AX UK
| | - Francesca Deflorian
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Herts AL7 3AX UK
| | - Stephanie Federico
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Piazzale Europa, 34127 Trieste, Italy
| | - Giampiero Spalluto
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Piazzale Europa, 34127 Trieste, Italy
| | - Robert M. Cooke
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Herts AL7 3AX UK
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, Padua, Italy
| | - Jonathan S. Mason
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Herts AL7 3AX UK
| | - Andrea Bortolato
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Herts AL7 3AX UK
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9
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Vagias A, Sergelen K, Koynov K, Košovan P, Dostalek J, Jonas U, Knoll W, Fytas G. Diffusion and Permeation of Labeled IgG in Grafted Hydrogels. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b00514] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- A. Vagias
- Max Planck Institute
for Polymer Research, Ackermannweg
10, 55128 Mainz, Germany
| | - K. Sergelen
- Biosensor
Technologies, AIT-Austrian Institute of Technology GmbH, Muthgasse
11, Wien 1190, Austria
- International
Graduate School on Bionanotechnology, University of Natural Resources
and Life Sciences, Nanyang Technological University, Singapore 639798
| | - K. Koynov
- Max Planck Institute
for Polymer Research, Ackermannweg
10, 55128 Mainz, Germany
| | - P. Košovan
- Department
of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - J. Dostalek
- Biosensor
Technologies, AIT-Austrian Institute of Technology GmbH, Muthgasse
11, Wien 1190, Austria
| | - U. Jonas
- Macromolecular
Chemistry, Department Chemistry - Biology, University of Siegen, 57076 Siegen, Germany
| | - W. Knoll
- Biosensor
Technologies, AIT-Austrian Institute of Technology GmbH, Muthgasse
11, Wien 1190, Austria
| | - G. Fytas
- Max Planck Institute
for Polymer Research, Ackermannweg
10, 55128 Mainz, Germany
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10
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Multia E, Sirén H, Andersson K, Samuelsson J, Forssén P, Fornstedt T, Öörni K, Jauhiainen M, Riekkola ML. Thermodynamic and kinetic approaches for evaluation of monoclonal antibody - Lipoprotein interactions. Anal Biochem 2017; 518:25-34. [DOI: 10.1016/j.ab.2016.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 09/30/2016] [Accepted: 10/26/2016] [Indexed: 11/16/2022]
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11
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Real-time and label-free analysis of binding thermodynamics of carbohydrate-protein interactions on unfixed cancer cell surfaces using a QCM biosensor. Sci Rep 2015; 5:14066. [PMID: 26369583 PMCID: PMC4570189 DOI: 10.1038/srep14066] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/17/2015] [Indexed: 11/08/2022] Open
Abstract
A novel approach to the study of binding thermodynamics and kinetics of carbohydrate-protein interactions on unfixed cancer cell surfaces using a quartz crystal microbalance (QCM) biosensor was developed, in which binding events take place at the cell surface, more closely mimicking a biologically relevant environment. In this study, colon adenocarcinoma cells (KM-12) and ovary adenocarcinoma cells (SKOV-3) grew on the optimized polystyrene-coated biosensor chip without fixation. The association and dissociation between the cell surface carbohydrates and a range of lectins, including WGA, Con A, UEA-I, GS-II, PNA and SBA, were monitored in real time and without label for evaluation of cell surface glycosylation. Furthermore, the thermodynamic and kinetic parameters of the interaction between lectins and cell surface glycan were studied, providing detailed information about the interactions, such as the association rate constant, dissociation rate constant, affinity constant, as well as the changes of entropy, enthalpy and Gibbs free energy. This application provides an insight into the cell surface glycosylation and the complex molecular recognition on the intact cell surface, which may have impacts on disease diagnosis and drug discovery.
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12
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Abstract
Protein tyrosine kinases differ widely in their propensity to undergo rearrangements
of the N-terminal Asp–Phe–Gly (DFG) motif of the activation
loop, with some, including FGFR1 kinase, appearing refractory to this so-called
‘DFG flip'. Recent inhibitor-bound structures have unexpectedly
revealed FGFR1 for the first time in a ‘DFG-out' state. Here we
use conformationally selective inhibitors as chemical probes for interrogation of
the structural and dynamic features that appear to govern the DFG flip in FGFR1. Our
detailed structural and biophysical insights identify contributions from altered
dynamics in distal elements, including the αH helix, towards the
outstanding stability of the DFG-out complex with the inhibitor ponatinib. We
conclude that the αC-β4 loop and ‘molecular
brake' regions together impose a high energy barrier for this
conformational rearrangement, and that this may have significance for maintaining
autoinhibition in the non-phosphorylated basal state of FGFR1. Receptor tyrosine kinases are key mediators of cell proliferation
that have been implicated in several disease states for which they represent promising
drug targets. Here the authors determine the thermodynamic basis for the low propensity
of FGFR1 to access the DFG-Phe-out conformation required to bind type-II
inhibitors.
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13
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Redhead M, Satchell R, Morkūnaitė V, Swift D, Petrauskas V, Golding E, Onions S, Matulis D, Unitt J. A combinatorial biophysical approach; FTSA and SPR for identifying small molecule ligands and PAINs. Anal Biochem 2015; 479:63-73. [PMID: 25837771 DOI: 10.1016/j.ab.2015.03.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 03/06/2015] [Accepted: 03/11/2015] [Indexed: 10/23/2022]
Abstract
Biophysical methods have emerged as attractive screening techniques in drug discovery both as primary hit finding methodologies, as in the case of weakly active compounds such as fragments, and as orthogonal methods for hit validation for compounds discovered through conventional biochemical or cellular assays. Here we describe a dual method employing fluorescent thermal shift assay (FTSA), also known as differential scanning fluorimetry (DSF) and surface plasmon resonance (SPR), to interrogate ligands of the kinase p38α as well as several known pan-assay interference compounds (PAINs) such as aggregators, redox cyclers, and fluorescence quenchers. This combinatorial approach allows for independent verification of several biophysical parameters such as KD, kon, koff, ΔG, ΔS, and ΔH, which may further guide chemical development of a ligand series. Affinity values obtained from FTSA curves allow for insight into compound binding compared with reporting shifts in melting temperature. Ligand-p38 interaction data were in good agreement with previous literature. Aggregators and fluorescence quenchers appeared to reduce fluorescence signal in the FTSAs, causing artificially high shifts in Tm values, whereas redox compounds caused either shifts in affinity that did not agree between FTSA and SPR or a depression of FTSA signal.
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Affiliation(s)
- M Redhead
- Bioscience Department, Sygnature Discovery, BioCity, Nottingham NG1 1GF, UK.
| | - R Satchell
- Bioscience Department, Sygnature Discovery, BioCity, Nottingham NG1 1GF, UK
| | - V Morkūnaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania; Department of Neurobiology and Biophysics, Faculty of Natural Sciences, Vilnius University, Vilnius 03101, Lithuania
| | - D Swift
- Bioscience Department, Sygnature Discovery, BioCity, Nottingham NG1 1GF, UK
| | - V Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania
| | - E Golding
- Bioscience Department, Sygnature Discovery, BioCity, Nottingham NG1 1GF, UK
| | - S Onions
- Chemistry Department, Sygnature Discovery, BioCity, Nottingham NG1 1GF, UK
| | - D Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania.
| | - J Unitt
- Bioscience Department, Sygnature Discovery, BioCity, Nottingham NG1 1GF, UK.
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14
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Six amino acid residues in a 1200 Å2 interface mediate binding of factor VIII to an IgG4κ inhibitory antibody. PLoS One 2015; 10:e0116577. [PMID: 25615825 PMCID: PMC4304825 DOI: 10.1371/journal.pone.0116577] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/10/2014] [Indexed: 02/03/2023] Open
Abstract
The development of neutralizing anti-factor VIII (FVIII) antibodies complicates the treatment of many hemophilia A patients. The C-terminal C2 domain is a particularly antigenic FVIII region. A crystal structure of recombinant FVIII-C2 bound to an Fab fragment of the patient-derived monoclonal antibody BO2C11, which recognizes an immunodominant inhibitor epitope on FVIII and blocks its ability to bind von Willebrand factor (VWF) and phospholipids, revealed that 15 amino acids in FVIII contact this antibody. Forty-three recombinant FVIII-C2 proteins, each with a surface-exposed side chain mutated to alanine or another residue, were generated, and surface plasmon resonance studies were carried out to evaluate effects of these substitutions on BO2C11/FVIII-C2 binding affinity. Thermodynamic analysis of experiments carried out at three temperatures indicated that one beta hairpin turn at the antigen-antibody interface (FVIII-F2196, N2198, M2199 and F2200) plus two non-contiguous arginines (FVIII-R2215 and R2220), contributed appreciably to the affinity. B-domain-deleted (BDD) FVIII-F2196A, FVIII-F2196K and FVIII-M2199A were generated and characterized. Their pro-coagulant activities and binding to VWF were similar to those of WT-BDD-FVIII, and FVIII-F2196K avoided neutralization by BO2C11 and murine inhibitory mAb 1B5. This study suggests specific sites for amino acid substitutions to rationally design FVIII variants capable of evading immunodominant neutralizing anti-FVIII antibodies.
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15
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Kurzątkowska K, Mielecki M, Grzelak K, Verwilst P, Dehaen W, Radecki J, Radecka H. Immobilization of His-tagged kinase JAK2 onto the surface of a plasmon resonance gold disc modified with different copper (II) complexes. Talanta 2014; 130:336-41. [DOI: 10.1016/j.talanta.2014.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 07/01/2014] [Accepted: 07/03/2014] [Indexed: 12/01/2022]
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16
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Oshiro S, Honda S. Imparting albumin-binding affinity to a human protein by mimicking the contact surface of a bacterial binding protein. ACS Chem Biol 2014; 9:1052-60. [PMID: 24533528 DOI: 10.1021/cb400946m] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Attachment of a bacterial albumin-binding protein module is an attractive strategy for extending the plasma residence time of protein therapeutics. However, a protein fused with such a bacterial module could induce unfavorable immune reactions. To address this, we designed an alternative binding protein by imparting albumin-binding affinity to a human protein using molecular surface grafting. The result was a series of human-derived 6 helix-bundle proteins, one of which specifically binds to human serum albumin (HSA) with adequate affinity (KD = 100 nM). The proteins were designed by transferring key binding residues of a bacterial albumin-binding module, Finegoldia magna protein G-related albumin-binding domain (GA) module, onto the human protein scaffold. Despite 13-15 mutations, the designed proteins maintain the original secondary structure by virtue of careful grafting based on structural informatics. Competitive binding assays and thermodynamic analyses of the best binders show that the binding mode resembles that of the GA module, suggesting that the contacting surface of the GA module is mimicked well on the designed protein. These results indicate that the designed protein may act as an alternative low-risk binding module to HSA. Furthermore, molecular surface grafting in combination with structural informatics is an effective approach for avoiding deleterious mutations on a target protein and for imparting the binding function of one protein onto another.
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Affiliation(s)
- Satoshi Oshiro
- Department
of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Shinya Honda
- Department
of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Biomedical
Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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17
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Azizoğlu S, Kizilel R, Marušič M, Kavakli IH, Erman B, Kizilel S. Computational and experimental investigation of DNA repair protein photolyase interactions with low molecular weight drugs. J Mol Recognit 2013; 26:297-307. [PMID: 23657985 DOI: 10.1002/jmr.2258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 09/21/2012] [Accepted: 11/28/2012] [Indexed: 11/06/2022]
Abstract
This paper reports the previously unknown interactions between eight low molecular weight commercially available drugs (130-800 Da) and DNA repair protein photolyase using computational docking simulations and surface plasmon resonance (SPR) experiments. Theoretical dissociation constants, K(d), obtained from molecular docking simulations were compared with the values found from SPR experiments. Among the eight drugs analyzed, computational and experimental values showed similar binding affinities between selected drug and protein pairs. We found no significant differences in binding interactions between pure and commercial forms of the drug lornoxicam and DNA photolyase. Among the eight drugs studied, prednisone, desloratadine, and azelastine exhibited the highest binding affinity (K(d) = 1.65, 2.05, and 8.47 μM, respectively) toward DNA photolyase. Results obtained in this study are promising for use in the prediction of unknown interactions of common drugs with specific proteins such as human clock protein cryptochrome.
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Affiliation(s)
- Selimcan Azizoğlu
- Koç University, College of Engineering, Chemical and Biological Engineering, Istanbul, 34450, Turkey
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18
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Arvinte T, Palais C, Green-Trexler E, Gregory S, Mach H, Narasimhan C, Shameem M. Aggregation of biopharmaceuticals in human plasma and human serum: implications for drug research and development. MAbs 2013; 5:491-500. [PMID: 23571158 PMCID: PMC4169040 DOI: 10.4161/mabs.24245] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Analytical methods based on light microscopy, 90° light-scattering and surface plasmon resonance (SPR) allowed the characterization of aggregation that can occur when antibodies are mixed with human plasma. Light microscopy showed that aggregates formed when human plasma was mixed with 5% dextrose solutions of Herceptin® (trastuzumab) or Avastin® (bevacizumab) but not Remicade® (infliximab). The aggregates in the plasma-Herceptin®-5% dextrose solution were globular, size range 0.5–9 μm, with a mean diameter of 4 μm. The aggregates in the plasma-Avastin®-5% dextrose samples had a mean size of 2 μm. No aggregation was observed when 0.9% NaCl solutions of Herceptin®, Avastin® and Remicade® were mixed with human plasma. 90° light-scattering measurements showed that aggregates were still present 2.5 h after mixing Herceptin® or Avastin® with 5% dextrose-plasma solution. A SPR method was utilized to qualitatively describe the extent of interactions of surface-bound antibodies with undiluted human serum. Increased binding was observed in the case of Erbitux® (cetuximab), whereas no binding was measured for Humira® (adalimumab). The binding of sera components to 13 monoclonal antibodies was measured and correlated with known serum binding properties of the antibodies. The data presented in this paper provide analytical methods to study the intrinsic and buffer-dependent aggregation tendencies of therapeutic proteins when mixed with human plasma and serum.
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Affiliation(s)
- Tudor Arvinte
- Therapeomic Inc.; Basel, Switzerland; School of Pharmaceutical Sciences; University of Geneva; University of Lausanne; Geneva, Switzerland
| | | | - Erin Green-Trexler
- Vaccine Drug Product Development; Merck Research Laboratories; West Point, PA USA
| | - Sonia Gregory
- Vaccine Drug Product Development; Merck Research Laboratories; West Point, PA USA
| | - Henryk Mach
- Vaccine Drug Product Development; Merck Research Laboratories; West Point, PA USA
| | | | - Mohammed Shameem
- Sterile Product Development; Merck Research Laboratories; Summit, NJ USA
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19
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Esseghaier C, Ng A, Zourob M. A novel and rapid assay for HIV-1 protease detection using magnetic bead mediation. Biosens Bioelectron 2013; 41:335-41. [DOI: 10.1016/j.bios.2012.08.049] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/20/2012] [Accepted: 08/22/2012] [Indexed: 10/27/2022]
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20
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Kizilel R, Demir E, Azizoglu S, Asımgi H, Kavakli IH, Kizilel S. Investigation of real-time photorepair activity on DNA via surface plasmon resonance. PLoS One 2012; 7:e44392. [PMID: 22952969 PMCID: PMC3430658 DOI: 10.1371/journal.pone.0044392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 08/06/2012] [Indexed: 11/18/2022] Open
Abstract
The cyclobutane pyrimidine dimer (CPD) and 6–4 lesion formations along with the specific breaks on strands are the most common type of DNA damage caused by Ultraviolet light (UV) irradiation. CPD photolyase I and II construct two subfamilies of flavoproteins, which have recognition and repair capabilities of CPD sites on both single stranded (ssDNA) and double stranded DNA (dsDNA) with the aid of blue light energy. The other types of flavoprotein family consist of cryptochromes (CRY) that act as photoreceptors in plants, or circadian rhythm regulators in animals. Recent findings showed that a specific type of Cryptochrome-Drosophila, Arabidopsis, Synechocystis, Human (CRY-DASH) has photorepair activity on ssDNA. In this work, real-time interactions between CRY-DASH and ss/dsDNA as well as the interactions between Vibrio cholerae photolyase (VcPHR) and ss/dsDNA were investigated using Surface Plasmon Resonance (SPR). The interactions were then characterized and compared in order to investigate the effect of different types of flavoprotein on UV damaged ss/dsDNA. SPR results confirm the specific binding of VcPHR and CRY-DASH with UV treated DNA. This study is the first instance to quantify the interactions of UV treated and untreated DNA with flavoproteins.
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Affiliation(s)
- Rıza Kizilel
- Chemical and Biological Engineering, Koc University, Sariyer, Istanbul, Turkey
- * E-mail: (SK); (IHK); (RK)
| | - Enis Demir
- Chemical and Biological Engineering, Koc University, Sariyer, Istanbul, Turkey
| | - Selimcan Azizoglu
- Chemical and Biological Engineering, Koc University, Sariyer, Istanbul, Turkey
| | - Hande Asımgi
- Chemical and Biological Engineering, Koc University, Sariyer, Istanbul, Turkey
- Material Science and Engineering, Koc University, Sariyer, Istanbul, Turkey
| | - Ibrahim Halil Kavakli
- Chemical and Biological Engineering, Koc University, Sariyer, Istanbul, Turkey
- Material Science and Engineering, Koc University, Sariyer, Istanbul, Turkey
- Molecular Biology and Genetics, Koc University, Sariyer, Istanbul, Turkey
- * E-mail: (SK); (IHK); (RK)
| | - Seda Kizilel
- Chemical and Biological Engineering, Koc University, Sariyer, Istanbul, Turkey
- Material Science and Engineering, Koc University, Sariyer, Istanbul, Turkey
- * E-mail: (SK); (IHK); (RK)
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21
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Jiménez-Castells C, Defaus S, Moise A, Przbylski M, Andreu D, Gutiérrez-Gallego R. Surface-Based and Mass Spectrometric Approaches to Deciphering Sugar–Protein Interactions in a Galactose-Specific Agglutinin. Anal Chem 2012; 84:6515-20. [DOI: 10.1021/ac300766z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Carmen Jiménez-Castells
- Department of Experimental
and
Health Sciences, Pompeu Fabra University, Barcelona Biomedical Research Park, 08003 Barcelona, Spain
| | - Sira Defaus
- Department of Experimental
and
Health Sciences, Pompeu Fabra University, Barcelona Biomedical Research Park, 08003 Barcelona, Spain
| | - Adrian Moise
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Michael Przbylski
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - David Andreu
- Department of Experimental
and
Health Sciences, Pompeu Fabra University, Barcelona Biomedical Research Park, 08003 Barcelona, Spain
| | - Ricardo Gutiérrez-Gallego
- Department of Experimental
and
Health Sciences, Pompeu Fabra University, Barcelona Biomedical Research Park, 08003 Barcelona, Spain
- Bio-analysis group, Neuroscience
Research Program, IMIM-Parc Salut Mar,
Barcelona Biomedical Research Park, 08003 Barcelona, Spain
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22
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Schräml M, von Proff L. Temperature-dependent antibody kinetics as a tool in antibody lead selection. Methods Mol Biol 2012; 901:183-94. [PMID: 22723102 DOI: 10.1007/978-1-61779-931-0_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Antibody-antigen interactions can principally be classified into three different temperature-dependent kinetic rate profiles. The affinity K (D) can persist, decrease, or increase in the temperature gradient. Today, the impact of temperature-dependent antibody kinetics is recognized, especially as part of the development of best in class monoclonal antibodies. Here, a robust surface plasmon resonance-based protocol is presented, which describes a sensitive temperature-dependent kinetic measurement and evaluation method.
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23
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Wakayama J, Sugiyama S. Evaluation of Temperature Effect on the Interaction between β-Lactoglobulin and Anti-β-lactoglobulin Antibody by Atomic Force Microscopy. Biochemistry 2011; 51:32-42. [DOI: 10.1021/bi201245k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun’ichi Wakayama
- Nano-Biotechnology Laboratory, Food
Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Shigeru Sugiyama
- Nano-Biotechnology Laboratory, Food
Engineering Division, National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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24
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Matsumoto-Takasaki A, Hanashima S, Aoki A, Yuasa N, Ogawa H, Sato R, Kawakami H, Mizuno M, Nakada H, Yamaguchi Y, Fujita-Yamaguchi Y. Surface plasmon resonance and NMR analyses of anti Tn-antigen MLS128 monoclonal antibody binding to two or three consecutive Tn-antigen clusters. J Biochem 2011; 151:273-82. [DOI: 10.1093/jb/mvr138] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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25
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Huot JL, Fischer F, Corbeil J, Madore E, Lorber B, Diss G, Hendrickson TL, Kern D, Lapointe J. Gln-tRNAGln synthesis in a dynamic transamidosome from Helicobacter pylori, where GluRS2 hydrolyzes excess Glu-tRNAGln. Nucleic Acids Res 2011; 39:9306-15. [PMID: 21813455 PMCID: PMC3241645 DOI: 10.1093/nar/gkr619] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In many bacteria and archaea, an ancestral pathway is used where asparagine and glutamine are formed from their acidic precursors while covalently linked to tRNAAsn and tRNAGln, respectively. Stable complexes formed by the enzymes of these indirect tRNA aminoacylation pathways are found in several thermophilic organisms, and are called transamidosomes. We describe here a transamidosome forming Gln-tRNAGln in Helicobacter pylori, an ε-proteobacterium pathogenic for humans; this transamidosome displays novel properties that may be characteristic of mesophilic organisms. This ternary complex containing the non-canonical GluRS2 specific for Glu-tRNAGln formation, the tRNA-dependent amidotransferase GatCAB and tRNAGln was characterized by dynamic light scattering. Moreover, we observed by interferometry a weak interaction between GluRS2 and GatCAB (KD = 40 ± 5 µM). The kinetics of Glu-tRNAGln and Gln-tRNAGln formation indicate that conformational shifts inside the transamidosome allow the tRNAGln acceptor stem to interact alternately with GluRS2 and GatCAB despite their common identity elements. The integrity of this dynamic transamidosome depends on a critical concentration of tRNAGln, above which it dissociates into separate GatCAB/tRNAGln and GluRS2/tRNAGln complexes. Ester bond protection assays show that both enzymes display a good affinity for tRNAGln regardless of its aminoacylation state, and support a mechanism where GluRS2 can hydrolyze excess Glu-tRNAGln, ensuring faithful decoding of Gln codons.
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Affiliation(s)
- Jonathan L Huot
- Département de Biochimie, de Microbiologie et de Bio-informatique, PROTEO et IBIS, Université Laval, 1045 av de la Médecine, Québec, Québec, Canada
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26
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Dolatshahi-Pirouz A, Kolman N, Arpanaei A, Jensen T, Foss M, Chevallier J, Kingshott P, Baas J, Søballe K, Besenbacher F. The adsorption characteristics of osteopontin on hydroxyapatite and gold. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2011. [DOI: 10.1016/j.msec.2010.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Edink E, Rucktooa P, Retra K, Akdemir A, Nahar T, Zuiderveld O, van Elk R, Janssen E, van Nierop P, van Muijlwijk-Koezen J, Smit AB, Sixma TK, Leurs R, de Esch IJP. Fragment Growing Induces Conformational Changes in Acetylcholine-Binding Protein: A Structural and Thermodynamic Analysis. J Am Chem Soc 2011; 133:5363-71. [DOI: 10.1021/ja110571r] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ewald Edink
- Leiden/Amsterdam Center of Drug
Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences,
VU University Amsterdam, The Netherlands
| | - Prakash Rucktooa
- Divison of Biochemistry, Netherlands
Cancer Institute, The Netherlands
| | - Kim Retra
- Leiden/Amsterdam Center of Drug
Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences,
VU University Amsterdam, The Netherlands
| | - Atilla Akdemir
- Leiden/Amsterdam Center of Drug
Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences,
VU University Amsterdam, The Netherlands
| | - Tariq Nahar
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics & Cognitive Research, VU University Amsterdam, The Netherlands
| | - Obbe Zuiderveld
- Leiden/Amsterdam Center of Drug
Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences,
VU University Amsterdam, The Netherlands
| | - René van Elk
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics & Cognitive Research, VU University Amsterdam, The Netherlands
| | - Elwin Janssen
- Department of Chemistry and
Pharmaceutical Sciences, VU University Amsterdam, The Netherlands
| | - Pim van Nierop
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics & Cognitive Research, VU University Amsterdam, The Netherlands
| | - Jacqueline van Muijlwijk-Koezen
- Leiden/Amsterdam Center of Drug
Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences,
VU University Amsterdam, The Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics & Cognitive Research, VU University Amsterdam, The Netherlands
| | - Titia K. Sixma
- Divison of Biochemistry, Netherlands
Cancer Institute, The Netherlands
| | - Rob Leurs
- Leiden/Amsterdam Center of Drug
Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences,
VU University Amsterdam, The Netherlands
| | - Iwan J. P. de Esch
- Leiden/Amsterdam Center of Drug
Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences,
VU University Amsterdam, The Netherlands
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28
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Walsh STR. A biosensor study indicating that entropy, electrostatics, and receptor glycosylation drive the binding interaction between interleukin-7 and its receptor. Biochemistry 2010; 49:8766-78. [PMID: 20815339 DOI: 10.1021/bi101050h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The interaction between interleukin-7 (IL-7) and its α-receptor, IL-7Rα, plays fundamental roles in the development, survival, and homeostasis of B- and T-cells. N-Linked glycosylation of human IL-7Rα enhances its binding affinity for human IL-7 300-fold versus that of the nonglycosylated receptor through an allosteric mechanism. The N-glycans of IL-7Rα do not participate directly in the binding interface with IL-7. This biophysical study involves dissection of the properties of binding of IL-7 to both nonglycosylated and glycosylated forms of the IL-7Rα extracellular domain (ECD) as functions of salt, pH, and temperature using surface plasmon resonance (SPR) spectroscopy. Interactions of IL-7 with both IL-7Rα variants display weaker binding affinities with increasing salt concentrations primarily reflected by changes in the first on rates of a two-step reaction pathway. The electrostatic parameter of the IL-7-IL-7Rα interaction is not driven by complementary charge interactions through residues at the binding interface or N-glycan composition of IL-7Rα, but presumably by favorable global charges of the two proteins. van't Hoff analysis indicates both IL-7-IL-7Rα interactions are driven by large favorable entropy changes and smaller unfavorable (nonglycosylated complex) and favorable (glycosylated complex) enthalpy changes. Eyring analysis of the IL-7-IL-7Rα interactions reveals different reaction pathways and barriers for the transition-state thermodynamics with the enthalpy and entropy changes of IL-7 binding to nonglycosylated and glycosylated IL-7Rα. There were no discernible heat capacity changes for the equilibrium or transition-state binding thermodynamics of the IL-7-IL-7Rα interactions. The results suggest that the unbound nonglycosylated IL-7Rα samples an extensive conformational landscape relative to the unbound glycosylated IL-7Rα, potentially explaining the switch from a "conformationally controlled" reaction (k(1) ∼ 10(2) M(-1) s(-1)) for the nonglycosylated interaction to a "diffusion-controlled" reaction (k(1) ∼ 10(6) M(-1) s(-1)) for the glycosylated interaction. Thus, a large favorable entropy change, a global favorable electrostatic component, and glycosylation of the receptor, albeit not at the interface, contribute significantly to the interaction between IL-7 and the IL-7Rα ECD.
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Affiliation(s)
- Scott T R Walsh
- Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.
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29
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Mesch S, Moser D, Strasser DS, Kelm A, Cutting B, Rossato G, Vedani A, Koliwer-Brandl H, Wittwer M, Rabbani S, Schwardt O, Kelm S, Ernst B. Low Molecular Weight Antagonists of the Myelin-Associated Glycoprotein: Synthesis, Docking, and Biological Evaluation. J Med Chem 2010; 53:1597-615. [DOI: 10.1021/jm901517k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefanie Mesch
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Delia Moser
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Daniel S. Strasser
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Antje Kelm
- Department of Physiological Biochemistry, University of Bremen, D-28334 Bremen, Germany
| | - Brian Cutting
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Gianluca Rossato
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Angelo Vedani
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | | | - Matthias Wittwer
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Said Rabbani
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Oliver Schwardt
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Soerge Kelm
- Department of Physiological Biochemistry, University of Bremen, D-28334 Bremen, Germany
| | - Beat Ernst
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
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Acchione M, Lipschultz CA, DeSantis ME, Shanmuganathan A, Li M, Wlodawer A, Tarasov S, Smith-Gill SJ. Light chain somatic mutations change thermodynamics of binding and water coordination in the HyHEL-10 family of antibodies. Mol Immunol 2009; 47:457-64. [PMID: 19781789 DOI: 10.1016/j.molimm.2009.08.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 08/28/2009] [Indexed: 01/14/2023]
Abstract
Thermodynamic and structural studies addressed the increased affinity due to L-chain somatic mutations in the HyHEL-10 family of affinity matured IgG antibodies, using ITC, SPR with van't Hoff analysis, and X-ray crystallography. When compared to the parental antibody H26L26, the H26L10 and H26L8 chimeras binding to lysozyme showed an increase in favorable DeltaG(o) of -1.2+/-0.1 kcal mol(-1) and -1.3+/-0.1 kcal mol(-1), respectively. Increase in affinity of the H26L10 chimera was due to a net increase in favorable enthalpy change with little difference in change in entropy compared to H26L26. The H26L8 chimera exhibited the greatest increase in favorable enthalpy but also showed an increase in unfavorable entropy change, with the result being that the affinities of both chimeras were essentially equivalent. Site-directed L-chain mutants identified the shared somatic mutation S30G as the dominant contributor to increasing affinity to lysozyme. This mutation was not influenced by H-chain somatic mutations. Residue 30L is at the periphery of the binding interface and S30G effects an increase in hydrophobicity and decrease in H-bonding ability and size, but does not make any new energetically important antigen contacts. A new 1.2-A structure of the H10L10-HEL complex showed changes in the pattern of both inter- and intra-molecular water bridging with no other significant structural alterations near the binding interface compared to the H26L26-HEL complex. These results highlight the necessity for investigating both the structure and the thermodynamics associated with introduced mutations, in order to better assess and understand their impact on binding. Furthermore, it provides an important example of how backbone flexibility and water-bridging may favorably influence the thermodynamics of an antibody-antigen interaction.
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Affiliation(s)
- Mauro Acchione
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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31
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Jisa E, Graumann K, Jungbauer A. Proteins Accompanying the Estrogen Receptor α and β: A Model for Studying Protein Hetero-Complexes. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242420108992028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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32
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Cooper MA. Signal transduction profiling using label-free biosensors. J Recept Signal Transduct Res 2009; 29:224-33. [DOI: 10.1080/10799890903047825] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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33
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Mok W, Stylianopoulos T, Boucher Y, Jain RK. Mathematical modeling of herpes simplex virus distribution in solid tumors: implications for cancer gene therapy. Clin Cancer Res 2009; 15:2352-60. [PMID: 19318482 DOI: 10.1158/1078-0432.ccr-08-2082] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
PURPOSE Although oncolytic viral vectors show promise for the treatment of various cancers, ineffective initial distribution and propagation throughout the tumor mass often limit the therapeutic response. A mathematical model is developed to describe the spread of herpes simplex virus from the initial injection site. EXPERIMENTAL DESIGN The tumor is modeled as a sphere of radius R. The model incorporates reversible binding, interstitial diffusion, viral degradation, and internalization and physiologic parameters. Three species are considered as follows: free interstitial virus, virus bound to cell surfaces, and internalized virus. RESULTS This analysis reveals that both rapid binding and internalization as well as hindered diffusion contain the virus to the initial injection volume, with negligible spread to the surrounding tissue. Unfortunately, increasing the dose to saturate receptors and promote diffusion throughout the tumor is not a viable option: the concentration necessary would likely compromise safety. However, targeted modifications to the virus that decrease the binding affinity have the potential to increase the number of infected cells by 1.5-fold or more. An increase in the effective diffusion coefficient can result in similar gains. CONCLUSIONS This analysis suggests criteria by which the potential response of a tumor to oncolytic herpes simplex virus therapy can be assessed. Furthermore, it reveals the potential of modifications to the vector delivery method, physicochemical properties of the virus, and tumor extracellular matrix composition to enhance efficacy.
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Affiliation(s)
- Wilson Mok
- Department of Radiation Oncology, Edwin L Steele Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
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34
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Suzuki N, Tsumoto K, Hajicek N, Daigo K, Tokita R, Minami S, Kodama T, Hamakubo T, Kozasa T. Activation of leukemia-associated RhoGEF by Galpha13 with significant conformational rearrangements in the interface. J Biol Chem 2008; 284:5000-9. [PMID: 19074425 DOI: 10.1074/jbc.m804073200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The transient protein-protein interactions induced by guanine nucleotide-dependent conformational changes of G proteins play central roles in G protein-coupled receptor-mediated signaling systems. Leukemia-associated RhoGEF (LARG), a guanine nucleotide exchange factor for Rho, contains an RGS homology (RH) domain and Dbl homology/pleckstrin homology (DH/PH) domains and acts both as a GTPase-activating protein (GAP) and an effector for Galpha(13). However, the molecular mechanism of LARG activation upon Galpha(13) binding is not yet well understood. In this study, we analyzed the Galpha(13)-LARG interaction using cellular and biochemical methods, including a surface plasmon resonance (SPR) analysis. The results obtained using various LARG fragments demonstrated that active Galpha(13) interacts with LARG through the RH domain, DH/PH domains, and C-terminal region. However, an alanine substitution at the RH domain contact position in Galpha(13) resulted in a large decrease in affinity. Thermodynamic analysis revealed that binding of Galpha(13) proceeds with a large negative heat capacity change (DeltaCp degrees ), accompanied by a positive entropy change (DeltaS degrees ). These results likely indicate that the binding of Galpha(13) with the RH domain triggers conformational rearrangements between Galpha(13) and LARG burying an exposed hydrophobic surface to create a large complementary interface, which facilitates complex formation through both GAP and effector interfaces, and activates the RhoGEF. We propose that LARG activation is regulated by an induced-fit mechanism through the GAP interface of Galpha(13).
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Affiliation(s)
- Nobuchika Suzuki
- Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
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Jason-Moller L, Murphy M, Bruno J. Overview of Biacore systems and their applications. ACTA ACUST UNITED AC 2008; Chapter 19:Unit 19.13. [PMID: 18429302 DOI: 10.1002/0471140864.ps1913s45] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Surface plasmon resonance (SPR) allows for the investigation of the functional nature of binding interactions and provides detailed kinetic information across a wide range of molecular weights, including small molecules, all without the use of labels. Here the various Biacore instrument platforms and their primary uses, ranging from semi-automated systems designed for simple, flexible basic research to fully automated, high-throughput systems, and systems designed to function in regulated environments, are all highlighted. The available sensor chip surfaces and immobilization techniques are also discussed. Biacore SPR biosensors can be used for a wide variety of assays, including specificity, active concentration measurement, kinetics, and affinity and thermodynamic parameters. Biacore SPR biosensors, which measure real-time analysis of biospecific interactions without the use of labeled molecules, can be used for a wide variety of protein interaction assays. In this unit, examples and recommendations for studying protein interactions with a variety of molecules are provided. This unit also shows how the technology can be used to determine binding specificity, active concentration measurements, and the determination of kinetic and thermodynamic parameters.
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36
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Geitmann M, Danielson UH. Additional level of information about complex interaction between non-nucleoside inhibitor and HIV-1 reverse transcriptase using biosensor-based thermodynamic analysis. Bioorg Med Chem 2007; 15:7344-54. [PMID: 17870544 DOI: 10.1016/j.bmc.2007.08.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 07/27/2007] [Accepted: 08/03/2007] [Indexed: 11/29/2022]
Abstract
The thermodynamics of the interaction between mutant HIV-1 reverse transcriptase (K103N and Y181C) and a non-nucleoside reverse transcriptase inhibitor (NNRTI), the phenylethylthiazolylurea compound MIV-150, was obtained by determining the temperature dependence of the kinetic rate constants. Large entropic changes in the forward and backward steps of the isomerization between a non-binding competent and a binding competent conformation of the enzyme, as well as in the binding steps, implied the involvement of major structural rearrangements upon interaction with the inhibitor. Despite of the entropic character of the overall interaction, the equilibrium for the binding of inhibitor was found to be predominantly enthalpy-driven. The high affinity and the low affinity interactions of the heterogeneously interacting inhibitor showed different energetics in the analysis, revealing an expectedly higher enthalpic component for the high-affinity interaction. The thermodynamic profiles of the two enzyme variants displayed significant differences, which could not be derived from their kinetics at a single temperature.
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Affiliation(s)
- Matthis Geitmann
- Department of Biochemistry and Organic Chemistry, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden.
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37
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Li Y, Yan XP, Chen C, Xia YL, Jiang Y. Human Serum Albumin−Mercurial Species Interactions. J Proteome Res 2007; 6:2277-86. [PMID: 17489621 DOI: 10.1021/pr0700403] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Binding of metal ions to the heteroatomic sites of proteins is undoubtedly fundamental to their observed physiological effects. In this paper, the interactions of inorganic mercury (Hg2+), methylmercury (MeHg+), ethylmercury (EtHg+), and phenylmercury (PhHg+) with human serum albumin (HSA) were studied from the electrophoretic behaviors, stoichiometry, thermodynamics, and kinetics by using a new hybrid technique, capillary electrophoresis on-line coupled with electrothermal atomic absorption spectrometry (CE-ETAAS), together with the consequent structural information from circular dichroism and Raman spectroscopy. The stoichiometry (mercurial species to HSA) for the interactions of Hg2+, MeHg+, EtHg+, and PhHg+ with HSA was found to be 6:1, 4:1, 4:1, and 3:1, respectively. Two types of binding sites in HSA were observed for the binding of mercurial species with the orders of magnitude of binding constants of 10(7) and 10(6) L mol-1, respectively, showing strong affinity of mercurial species for HSA. The interactions of mercurial species with both types of binding sites in HSA are exothermic and thermodynamically favorable and are both enthalpically and entropically driven. The binding of mercurial species to HSA follows the first-order kinetics for mercurial species and zero-order kinetics for HSA with the apparent activation energy of 57-59 kJ mol-1. Among the four mercurial species examined, only Hg2+ induces the secondary structure transition of HSA. Mercury-HSA adducts are formed mainly through metal-sulfur binding with participation of C=O and/or C-N groups of amino acid residues in HSA molecules. The present work represents the most comprehensive study on the interactions between various mercurial species with HSA and provides new evidence for and insights into the interactions of mercurial species with HSA for further understanding of the toxicological effects of mercurial species.
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Affiliation(s)
- Yan Li
- Key Laboratory of Functional Polymer Materials (Nankai University), Ministry of Education; Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
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Wear MA, Walkinshaw MD. Thermodynamics of the cyclophilin-A/cyclosporin-A interaction: a direct comparison of parameters determined by surface plasmon resonance using Biacore T100 and isothermal titration calorimetry. Anal Biochem 2006; 359:285-7. [PMID: 17069746 DOI: 10.1016/j.ab.2006.08.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 08/30/2006] [Accepted: 08/31/2006] [Indexed: 12/01/2022]
Affiliation(s)
- Martin A Wear
- The Centre for Translational and Chemical Biology, The University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
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39
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Kim D, Kwak YG, Kang SH. Real-time observation of temperature-dependent protein–protein interactions using real-time dual-color detection system. Anal Chim Acta 2006; 577:163-70. [PMID: 17723667 DOI: 10.1016/j.aca.2006.06.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Revised: 06/15/2006] [Accepted: 06/18/2006] [Indexed: 10/24/2022]
Abstract
This study examined the ability of a real-time dual-color detection system to allow direct observations of the kinetics of temperature-dependent protein-protein interaction at a single-molecule level. The primary target protein was an Alexa Fluor 488-labeled actin conjugate, which had been pre-incubated with an unlabeled rabbit anti-actin antibody (IgG). The complementary fluorescent protein was Alexa Fluor 633-labeled goat anti-rabbit IgG antibody, which interacts with the rabbit anti-actin antibody (IgG) bound to the Alexa Fluor 488-labeled actin conjugate. The individual protein molecules labeled with different fluorescent dyes in solution were effectively focused, interacted with the other protein molecules at 500 aM, and detected directly in real-time using the dual-wavelength (lambda(ex)=488 and 635 nm) laser-induced fluorescence detection system. The kinetics of the protein-protein interactions were examined at different temperatures (12-32 degrees C). At concentrations in the aM range, the number of bound complex molecules through the protein-protein interaction decreased gradually with time at a given temperature, and increased with decreasing temperature at a set time. A high concentration (above 500 pM) of the protein sample caused aggregation and nonspecific binding of the protein molecules, even though the protein molecules were not an example of complementary binding. The results demonstrated that the real-time kinetics of a protein-protein interaction could be analyzed effectively at the single-molecule level without any time delay using the real-time dual-color detection system.
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Affiliation(s)
- Daekwang Kim
- Department of Chemistry, Chonbuk National University, Jeonju 561-756, Republic of Korea
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40
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Winzor DJ, Jackson CM. Interpretation of the temperature dependence of equilibrium and rate constants. J Mol Recognit 2006; 19:389-407. [PMID: 16897812 DOI: 10.1002/jmr.799] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The objective of this review is to draw attention to potential pitfalls in attempts to glean mechanistic information from the magnitudes of standard enthalpies and entropies derived from the temperature dependence of equilibrium and rate constants for protein interactions. Problems arise because the minimalist model that suffices to describe the energy differences between initial and final states usually comprises a set of linked equilibria, each of which is characterized by its own energetics. For example, because the overall standard enthalpy is a composite of those individual values, a positive magnitude for DeltaH(o) can still arise despite all reactions within the subset being characterized by negative enthalpy changes: designation of the reaction as being entropy driven is thus equivocal. An experimenter must always bear in mind the fact that any mechanistic interpretation of the magnitudes of thermodynamic parameters refers to the reaction model rather than the experimental system. For the same reason there is little point in subjecting the temperature dependence of rate constants for protein interactions to transition-state analysis. If comparisons with reported values of standard enthalpy and entropy of activation are needed, they are readily calculated from the empirical Arrhenius parameters.
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Affiliation(s)
- Donald J Winzor
- Department of Biochemistry, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.
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41
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Winzor DJ, Jackson CM. Interpretation of the temperature dependence of rate constants in biosensor studies. Anal Biochem 2005; 337:289-93. [PMID: 15691509 DOI: 10.1016/j.ab.2004.10.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Indexed: 10/26/2022]
Abstract
A comparison is made between Arrhenius and transition-state analyses of the temperature dependence of rate constants reported in four published biosensor studies. Although the Eyring transition-state theory seemingly affords a more definitive solution to the problem of characterizing the activation energetics, the analysis is equivocal because of inherent assumptions about reaction mechanism and the magnitude of the transmission coefficient. In view of those uncertainties it is suggested that a preferable course of action entails reversion to the empirical Arrhenius analysis with regard to the energy of activation and a preexponential factor. The former is essentially equivalent to the enthalpy of activation, whereas the magnitude of the latter indicates directly the extent of disparity between the frequency of product formation and the universal frequency factor (temperature multiplied by the ratio of the Boltzmann and Planck constants) and hence the likelihood of a more complicated kinetic mechanism than that encompassed by the Eyring transition-state theory.
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Affiliation(s)
- Donald J Winzor
- Department of Biochemistry, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Qld. 4072, Australia.
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42
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Dejaegere A, Choulier L, Lafont V, De Genst E, Altschuh D. Variations in Antigen−Antibody Association Kinetics as a Function of pH and Salt Concentration: A QSAR and Molecular Modeling Study. Biochemistry 2005; 44:14409-18. [PMID: 16262241 DOI: 10.1021/bi050986v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The relationship between three environmental factors (ionic strength, pH, and temperature) and antigen-antibody binding kinetics was investigated using QSAR (quantitative structure-activity relationship) and molecular modeling approaches. The interaction used for this analysis is that between the camel antibody fragment cAbLys3 and lysozyme. Binding kinetics were measured using a Biacore 2000 instrument, at NaCl concentrations between 50 and 500 mM, at pH's between 5 and 10, and at temperatures between 15 and 30 degrees C, according to multivariate experimental designs. Variations in kinetic on- and off-rate parameters were up to 400- and 16-fold, respectively. Mathematical models that relate log k(on) to experimental conditions were developed. They indicated an influence of all three factors, with a clear dependency between pH and NaCl concentration for their effect on k(on). These models were able to predict on-rate parameters under new experimental conditions. Titration calculations using continuum electrostatics were performed on the crystallographic structures of the isolated and bound proteins to gain structural insight for the on-rate enhancement observed at pH <6.5 and low salt concentrations. These calculations rule out electrostatic steering linked to global and/or local charge variations in the molecules as the factor responsible for the on-rate enhancement at low pH. His 111 of cAbLys3, located at the binding interface, can adopt two side chain orientations with different intramolecular contacts. The results of the calculations suggest an alternative mechanism whereby the conformation of the interfacial His 111 depends on the charge, and these differences in conformation may influence the solvation energy and the subsequent binding kinetics. Our results stress the complex relationship between environmental conditions and molecular binding properties.
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Affiliation(s)
- Annick Dejaegere
- UMR 7104, Structural Biology and Genomics Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 10142 F-67404 Illkirch Cedex, France
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43
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Yi-Min Q, Ni-Na P, Yong-Xing J, Zao-Ying L, Guo-Lin Z. Thermodynamic Analysis of the Interaction between Cationic Porphyrins and Human Serum Albumin by an Optical Biosensor. CHINESE J CHEM 2005. [DOI: 10.1002/cjoc.200591095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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44
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Dhalluin C, Ross A, Huber W, Gerber P, Brugger D, Gsell B, Senn H. Structural, Kinetic, and Thermodynamic Analysis of the Binding of the 40 kDa PEG−Interferon-α2aand Its Individual Positional Isomers to the Extracellular Domain of the Receptor IFNAR2. Bioconjug Chem 2005; 16:518-27. [PMID: 15898717 DOI: 10.1021/bc049780h] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type-I Interferons exert antiviral and antiproliferative activities through the binding to a common cell surface receptor comprising two subunits, IFNAR1 and IFNAR2. Human recombinant Interferon-alpha(2a) (IFNalpha(2a)) is a potent drug (Roferon-A) used to treat various cancers and viral diseases including Hepatitis B/C infections. To significantly improve the pharmacological properties of the drug, a pegylated form of IFNalpha(2a) was developed (PEGASYS). This 40 kDa PEG-conjugated IFNalpha(2a) ((40)PEG-IFNalpha(2a)) is obtained by the covalent binding of one 40 kDa branched PEG-polymer to a lysine side-chain of IFNalpha(2a). Here, we report the detailed structural, kinetic, and thermodynamic analysis of the binding to the extracellular domain of the receptor IFNAR2 of (40)PEG-IFNalpha(2a) and its isolated positional isomers modified at K31, K134, K131, K121, K164, and K70, respectively, in comparison with unmodified IFNalpha(2a). Our binding studies, using the surface plasmon resonance technique, show that the pegylation does not abolish the binding to the receptor, but significantly reduces the affinity mainly due to a change of the association rate. The results are supported by modeling and simulation of the binding, using Self-Avoiding-Walk calculations for the polymer conformations. A correlation between the structural parameters and the kinetic and thermodynamic parameters of the binding of the positional isomers could be established. For the Isomer-K31 and -K164, the PEG-polymer attachment point is located in proximity to the binding interface, and the isomers display affinity in the range 150-520 nM in an enthalpy-driven binding process. In contrast for the Isomer-K134, -K131, -K121, and -K70, the PEG-polymer is attached remotely from the binding interface, and the isomers exhibit a higher affinity (32-76 nM) in an entropy-driven binding process. This study constitutes an essential collection of knowledge on which the interaction of (40)PEG-IFNalpha(2a) and its positional isomers with its cellular receptors can be better understood.
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Affiliation(s)
- Christophe Dhalluin
- F. Hoffmann-La Roche AG, Department of Pharma Research, CH-4070 Basel, Switzerland
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45
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Darling RJ, Brault PA. Kinetic exclusion assay technology: characterization of molecular interactions. Assay Drug Dev Technol 2005; 2:647-57. [PMID: 15674023 DOI: 10.1089/adt.2004.2.647] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Characterization of intermolecular interactions in terms of affinity, binding kinetics, stoichiometry, specificity, and thermodynamics can facilitate the selection of lead compounds in the discovery and development of protein therapeutics. KinExA (Sapidyne Instruments, Inc., Boise, ID) is a relatively new technology that is gaining use in characterizing molecular interactions, particularly with respect to antibody therapeutics. KinExA offers a platform that allows the measurement of true equilibrium binding affinity and kinetics using unmodified molecules in solution phase. This is accomplished by using a solid-phase immobilized molecule to probe for free concentration of one interaction component after allowing sufficient time to reach equilibrium (affinity measurements), or under pre-equilibrium conditions (kinetics). In this review, the theory behind KinExA technology is discussed, and examples of applying this technology to antibody characterization are provided. Finally, a comparison among KinExA, Biacore (surface plasmon resonance), and isothermal titration calorimetry is presented, and potential future improvements and applications of KinExA are discussed.
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Affiliation(s)
- Ryan J Darling
- BioTechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Co., Indianapolis, IN 46285, USA.
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Freyhult E, Prusis P, Lapinsh M, Wikberg JES, Moulton V, Gustafsson MG. Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling. BMC Bioinformatics 2005; 6:50. [PMID: 15760465 PMCID: PMC555743 DOI: 10.1186/1471-2105-6-50] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2004] [Accepted: 03/10/2005] [Indexed: 12/05/2022] Open
Abstract
Background Proteochemometrics is a new methodology that allows prediction of protein function directly from real interaction measurement data without the need of 3D structure information. Several reported proteochemometric models of ligand-receptor interactions have already yielded significant insights into various forms of bio-molecular interactions. The proteochemometric models are multivariate regression models that predict binding affinity for a particular combination of features of the ligand and protein. Although proteochemometric models have already offered interesting results in various studies, no detailed statistical evaluation of their average predictive power has been performed. In particular, variable subset selection performed to date has always relied on using all available examples, a situation also encountered in microarray gene expression data analysis. Results A methodology for an unbiased evaluation of the predictive power of proteochemometric models was implemented and results from applying it to two of the largest proteochemometric data sets yet reported are presented. A double cross-validation loop procedure is used to estimate the expected performance of a given design method. The unbiased performance estimates (P2) obtained for the data sets that we consider confirm that properly designed single proteochemometric models have useful predictive power, but that a standard design based on cross validation may yield models with quite limited performance. The results also show that different commercial software packages employed for the design of proteochemometric models may yield very different and therefore misleading performance estimates. In addition, the differences in the models obtained in the double CV loop indicate that detailed chemical interpretation of a single proteochemometric model is uncertain when data sets are small. Conclusion The double CV loop employed offer unbiased performance estimates about a given proteochemometric modelling procedure, making it possible to identify cases where the proteochemometric design does not result in useful predictive models. Chemical interpretations of single proteochemometric models are uncertain and should instead be based on all the models selected in the double CV loop employed here.
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MESH Headings
- Algorithms
- Animals
- Computational Biology/methods
- Computer Simulation
- Data Interpretation, Statistical
- Humans
- Ligands
- Models, Biological
- Models, Chemical
- Models, Molecular
- Models, Statistical
- Models, Theoretical
- Oligonucleotide Array Sequence Analysis/methods
- Predictive Value of Tests
- Programming Languages
- Protein Binding
- Protein Conformation
- Rats
- Receptors, Adrenergic, alpha-1/chemistry
- Receptors, G-Protein-Coupled/chemistry
- Regression Analysis
- Reproducibility of Results
- Selection, Genetic
- Software
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Affiliation(s)
- Eva Freyhult
- The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, S-751 24 Uppsala, Sweden
| | - Peteris Prusis
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, S-751 24 Uppsala, Sweden
| | - Maris Lapinsh
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, S-751 24 Uppsala, Sweden
| | - Jarl ES Wikberg
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, S-751 24 Uppsala, Sweden
| | - Vincent Moulton
- The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, S-751 24 Uppsala, Sweden
| | - Mats G Gustafsson
- Department of Engineering Sciences, Uppsala University, Box 528, S-751 20 Uppsala, Sweden
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Gesellchen F, Zimmermann B, Herberg FW. Direct optical detection of protein-ligand interactions. Methods Mol Biol 2005; 305:17-46. [PMID: 15939992 DOI: 10.1385/1-59259-912-5:017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Direct optical detection provides an excellent means to investigate interactions of molecules in biological systems. The dynamic equilibria inherent to these systems can be described in greater detail by recording the kinetics of a biomolecular interaction. Optical biosensors allow direct detection of interaction patterns without the need for labeling. An overview covering several commercially available biosensors is given, with a focus on instruments based on surface plasmon resonance (SPR) and reflectometric interference spectroscopy (RIFS). Potential assay formats and experimental design, appropriate controls, and calibration procedures, especially when handling low molecular weight substances, are discussed. The single steps of an interaction analysis combined with practical tips for evaluation, data processing, and interpretation of kinetic data are described in detail. In a practical example, a step-by-step procedure for the analysis of a low molecular weight compound interaction with serum protein, determined on a commercial SPR sensor, is presented.
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Affiliation(s)
- Frank Gesellchen
- Department of Biochemistry, University of Kassel, Kassel, Germany
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48
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Feldhaus MJ, Siegel RW. Yeast display of antibody fragments: a discovery and characterization platform. J Immunol Methods 2004; 290:69-80. [PMID: 15261572 DOI: 10.1016/j.jim.2004.04.009] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2004] [Indexed: 10/26/2022]
Abstract
Yeast display of antibody fragments has proven to be an efficient and productive means for directed evolution of single-chain Fv (scFv) antibodies for increased affinity and thermal stability and, more recently, for the display and screening of a non-immune scFv and immune Fab libraries. A major strength of yeast display as a novel antibody discovery platform is the ability to characterize the binding properties, i.e., the affinity and epitope binding characteristics, of a clone without the need for subcloning, expression and purification of the scFv. This review focuses on novel attributes of yeast display for antibody engineering endeavors.
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Affiliation(s)
- Michael J Feldhaus
- Pacific Northwest National Laboratory, MSIN:K4-12, 902 Battelle Boulevard, P.O. Box 999, Richland, WA 99352, USA.
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Critchley P, Dimmock NJ. Binding of an influenza A virus to a neomembrane measured by surface plasmon resonance. Bioorg Med Chem 2004; 12:2773-80. [PMID: 15110858 DOI: 10.1016/j.bmc.2004.02.042] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2003] [Accepted: 02/27/2004] [Indexed: 11/20/2022]
Abstract
Neomembranes composed of either bovine brain lipid that contains sialoglycolipids or egg yolk lecithin that does not, were formed on an HPA sensor chip and used to study the binding of influenza A virus in real time by surface plasmon resonance. Virus bound only to the bovine brain lipid membrane. This was confirmed by an 84% reduction in virus binding after treatment of the neomembrane with neuraminidase. Binding was temperature dependent, being highest at 30-35 degrees C and lower at 10 degrees C. Surprisingly, the rate of complex formation was enhanced, rather than inhibited, by the presence of 1.34-25.2 x 10(6) molecules of free NANA per virus binding site and the rate of dissociation was lower suggesting that the complex was more stable. The free energy of association to form the transition complex was increased by 3 kJ mol(-1) and there was an almost 10-fold increase in the enthalpy of complex formation in the presence of free NANA. These results show the value of surface plasmon resonance for measuring complex molecular interactions in real time, and provide a model that can be used to study the effectiveness of inhibitors of attachment of influenza virus to its receptor molecules.
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Casper D, Bukhtiyarova M, Springman EB. A Biacore biosensor method for detailed kinetic binding analysis of small molecule inhibitors of p38α mitogen-activated protein kinase. Anal Biochem 2004; 325:126-36. [PMID: 14715293 DOI: 10.1016/j.ab.2003.10.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Protein kinases are emerging as one of the most intensely studied classes of enzymes as their central roles in physiologically and clinically important cellular signaling events become more clearly understood. We report here the development of a real-time, label-free method to study protein kinase inhibitor binding kinetics using surface plasmon resonance-based biomolecular interaction analysis (Biacore). Utilizing p38alpha mitogen-activated protein kinase as a model system, we studied the binding properties of two known small molecule p38alpha inhibitors (SB-203580 and SKF-86002). Direct coupling of p38alpha to the biosensor surface in the presence of a reversible structure-stabilizing ligand (SB-203580) consistently produced greater than 90% active protein on the biosensor surface. The dissociation and kinetic constants derived using this Biacore method are in excellent agreement with values determined by other methods. Additionally, we extend the method to study the thermodynamics of small molecule binding to p38alpha and derive a detailed thermodynamic reaction pathway for SB-203580. The Biacore method reported here provides an efficient way to directly and reproducibly examine dissociation constants, kinetics, and thermodynamics for small molecules binding to p38alpha and possibly other protein kinases. Immobilization in the presence of a stabilizing ligand may further represent a broadly applicable paradigm for creation of highly active biosensor surfaces.
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Affiliation(s)
- David Casper
- Department of Biochemistry, Locus Pharmaceuticals, Inc, Four Valley Square, 512 Township Line Road, Blue Bell, PA 19422, USA
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