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Baardsnes J, Paul-Roc B. SARS-CoV-2S-Protein-Ace2 Binding Analysis Using Surface Plasmon Resonance. Methods Mol Biol 2024; 2762:71-87. [PMID: 38315360 DOI: 10.1007/978-1-0716-3666-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Surface plasmon resonance (SPR) allows for the label-free determination of the binding affinity and rate constants of bimolecular interactions. Here, we describe the method used for the analysis of the Ace2-SARS-CoV2 S-protein interaction using indirect capture of the S-protein onto the SPR surface, and flowing monomeric Ace2. This method will allow for the determination of the rate constants for affinity, with additional analysis that is achievable using S-protein capture levels in conjunction with the sensorgram response for relative activity benchmarking.
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Affiliation(s)
- Jason Baardsnes
- Quality Attributes and Characterization, Human Health Therapeutics, National Research Council Canada, Montréal, QC, Canada.
| | - Béatrice Paul-Roc
- Quality Attributes and Characterization, Human Health Therapeutics, National Research Council Canada, Montréal, QC, Canada
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2
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Iwamoto M, Morito M, Oiki S, Nishitani Y, Yamamoto D, Matsumori N. Cardiolipin binding enhances KcsA channel gating via both its specific and dianion-monoanion interchangeable sites. iScience 2023; 26:108471. [PMID: 38077151 PMCID: PMC10709135 DOI: 10.1016/j.isci.2023.108471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/29/2023] [Accepted: 11/13/2023] [Indexed: 01/17/2024] Open
Abstract
KcsA is a potassium channel with a plethora of structural and functional information, but its activity in the KcsA-producing actinomycete membranes remains elusive. To determine lipid species involved in channel-modulation, a surface plasmon resonance (SPR)-based methodology, characterized by immobilization of membrane proteins under a membrane environment, was applied. Dianionic cardiolipin (CL) showed extremely higher affinity for KcsA than monoanionic lipids. The SPR experiments further demonstrated that CL bound not only to the N-terminal M0 helix, a lipid-sensor domain, but to the M0 helix-deleted mutant. In contrast, monoanionic lipids interacted primarily with the M0 helix. This indicates the presence of an alternative CL-binding site, plausibly in the transmembrane domain. Single-channel recordings demonstrated that CL enhanced channel opening in an M0-independent manner. Taken together, the action of monoanionic lipids is exclusively mediated by the M0 helix, while CL binds both the M0 helix and its specific site, further enhancing the channel activity.
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Affiliation(s)
- Masayuki Iwamoto
- Department of Molecular Neuroscience, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Masayuki Morito
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395 Japan
| | - Shigetoshi Oiki
- Biomedial Imaging Research Center, University of Fukui, Fukui 910-1193, Japan
| | - Yudai Nishitani
- Department of Applied Physics, Faculty of Science, Fukuoka University, Fukuoka 814-0180, Japan
| | - Daisuke Yamamoto
- Department of Applied Physics, Faculty of Science, Fukuoka University, Fukuoka 814-0180, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395 Japan
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3
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Impact of the temperature on the interactions between common variants of the SARS-CoV-2 receptor binding domain and the human ACE2. Sci Rep 2022; 12:11520. [PMID: 35798770 PMCID: PMC9261887 DOI: 10.1038/s41598-022-15215-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/21/2022] [Indexed: 11/28/2022] Open
Abstract
Several key mutations in the Spike protein receptor binding domain (RBD) have been identified to influence its affinity for the human Angiotensin-Converting Enzyme 2 (ACE2). Here, we perform a comparative study of the ACE2 binding to the wild type (Wuhan) RBD and some of its variants: Alpha B.1.1.7, Beta B.1.351, Delta B.1.617.2, Kappa B.1.617.1, B.1.1.7 + L452R and Omicron B.1.1.529. Using a coiled-coil mediated tethering approach of ACE2 in a novel surface plasmon resonance (SPR)-based assay, we measured interactions at different temperatures. Binding experiments at 10 °C enhanced the kinetic dissimilarities between the RBD variants and allowed a proper fit to a Langmuir 1:1 model with high accuracy and reproducibility, thus unraveling subtle differences within RBD mutants and ACE2 glycovariants. Our study emphasizes the importance of SPR-based assay parameters in the acquisition of biologically relevant data and offers a powerful tool to deepen our understanding of the role of the various RBD mutations in ACE2 interaction binding parameters.
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4
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On the Use of Surface Plasmon Resonance-Based Biosensors for Advanced Bioprocess Monitoring. Processes (Basel) 2021. [DOI: 10.3390/pr9111996] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Biomanufacturers are being incited by regulatory agencies to transition from a quality by testing framework, where they extensively test their product after their production, to more of a quality by design or even quality by control framework. This requires powerful analytical tools and sensors enabling measurements of key process variables and/or product quality attributes during production, preferably in an online manner. As such, the demand for monitoring technologies is rapidly growing. In this context, we believe surface plasmon resonance (SPR)-based biosensors can play a role in enabling the development of improved bioprocess monitoring and control strategies. The SPR technique has been profusely used to probe the binding behavior of a solution species with a sensor surface-immobilized partner in an investigative context, but its ability to detect binding in real-time and without a label has been exploited for monitoring purposes and is promising for the near future. In this review, we examine applications of SPR that are or could be related to bioprocess monitoring in three spheres: biotherapeutics production monitoring, vaccine monitoring, and bacteria and contaminant detection. These applications mainly exploit SPR’s ability to measure solution species concentrations, but performing kinetic analyses is also possible and could prove useful for product quality assessments. We follow with a discussion on the limitations of SPR in a monitoring role and how recent advances in hardware and SPR response modeling could counter them. Mainly, throughput limitations can be addressed by multi-detection spot instruments, and nonspecific binding effects can be alleviated by new antifouling materials. A plethora of methods are available for cell growth and metabolism monitoring, but product monitoring is performed mainly a posteriori. SPR-based biosensors exhibit potential as product monitoring tools from early production to the end of downstream processing, paving the way for more efficient production control. However, more work needs to be done to facilitate or eliminate the need for sample preprocessing and to optimize the experimental protocols.
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Yang HM, Yim B, Lee BH, Park Y, Kim YG, Kim J, Yoo D. New Tool for Rapid and Accurate Detection of Interleukin-2 and Soluble Interleukin-2 Receptor α in Cancer Diagnosis Using a Bioresponsive Microgel and Multivalent Protein Binding. ACS APPLIED MATERIALS & INTERFACES 2021; 13:33782-33789. [PMID: 34258987 DOI: 10.1021/acsami.1c04827] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Interleukin-2 (IL-2) and its α receptor in soluble form (sIL-2Rα) are considered biomarkers for cancers and immune-related diseases. Enzyme-linked immunosorbent assay is the most common method used to evaluate biomarkers in clinical practice; it is precise but time-consuming and involves complicated procedures. Here, we have developed a rapid yet accurate modality for cancer diagnosis that enables on-site evaluation of cancer markers, that is, IL-2 and sIL-2Rα, without complicated pretreatment of cancer patient-derived blood samples. Surface plasmon resonance and bioresponsive microgels conjugated with IL-2 receptors, that is, IL-2Rβ and IL-2Rγ, were utilized to measure IL-2 and sIL-2Rα levels via multivalent protein binding (MPB) between the ligands and their receptors. Our results showed that this novel method enables us to perform cancer diagnosis with a 1000-fold dilution of serum in 10 min. The advantage of MPB-based cancer diagnosis originates from its great selectivity for a target molecule and tolerance to a myriad of nonspecific substances in serum, which allows on-site clinical evaluation. Importantly, our finding implies that MPB-based cancer diagnosis provides a new paradigm not only for improving cancer treatment but also for evaluating a target molecule in unpurified and complex solutions such as blood.
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Affiliation(s)
- Hae Min Yang
- School of Chemical and Biological Engineering, and Institute of Chemical Process, Seoul National University, Seoul 08826, Republic of Korea
| | - Bora Yim
- R&D center, Scholar Foxtrot Co. Ltd., Seoul 02841, Republic of Korea
| | - Byung-Hyun Lee
- Department of Internal Medicine, Korea University College of Medicine, Anam Hospital, Seoul 02841, Republic of Korea
| | - Yongdoo Park
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Young Gyu Kim
- School of Chemical and Biological Engineering, and Institute of Chemical Process, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongseong Kim
- R&D center, Scholar Foxtrot Co. Ltd., Seoul 02841, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Dongwon Yoo
- School of Chemical and Biological Engineering, and Institute of Chemical Process, Seoul National University, Seoul 08826, Republic of Korea
- Center for Nanoparticle Research, Institute for Basic Science, Seoul 08826, Republic of Korea
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6
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On the Use of Surface Plasmon Resonance Biosensing to Understand IgG-FcγR Interactions. Int J Mol Sci 2021; 22:ijms22126616. [PMID: 34205578 PMCID: PMC8235063 DOI: 10.3390/ijms22126616] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 01/01/2023] Open
Abstract
Surface plasmon resonance (SPR)-based optical biosensors offer real-time and label-free analysis of protein interactions, which has extensively contributed to the discovery and development of therapeutic monoclonal antibodies (mAbs). As the biopharmaceutical market for these biologics and their biosimilars is rapidly growing, the role of SPR biosensors in drug discovery and quality assessment is becoming increasingly prominent. One of the critical quality attributes of mAbs is the N-glycosylation of their Fc region. Other than providing stability to the antibody, the Fc N-glycosylation influences immunoglobulin G (IgG) interactions with the Fcγ receptors (FcγRs), modulating the immune response. Over the past two decades, several studies have relied on SPR-based assays to characterize the influence of N-glycosylation upon the IgG-FcγR interactions. While these studies have unveiled key information, many conclusions are still debated in the literature. These discrepancies can be, in part, attributed to the design of the reported SPR-based assays as well as the methodology applied to SPR data analysis. In fact, the SPR biosensor best practices have evolved over the years, and several biases have been pointed out in the development of experimental SPR protocols. In parallel, newly developed algorithms and data analysis methods now allow taking into consideration complex biomolecular kinetics. In this review, we detail the use of different SPR biosensing approaches for characterizing the IgG-FcγR interactions, highlighting their merit and inherent experimental complexity. Furthermore, we review the latest SPR-derived conclusions on the influence of the N-glycosylation upon the IgG-FcγR interactions and underline the differences and similarities across the literature. Finally, we explore new avenues taking advantage of novel computational analysis of SPR results as well as the latest strategies to control the glycoprofile of mAbs during production, which could lead to a better understanding and modelling of the IgG-FcγRs interactions.
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Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology. PLoS Comput Biol 2021; 17:e1008169. [PMID: 33411763 PMCID: PMC7817036 DOI: 10.1371/journal.pcbi.1008169] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/20/2021] [Accepted: 11/24/2020] [Indexed: 01/31/2023] Open
Abstract
Streptococcus pyogenes (Group A streptococcus; GAS) is an important human pathogen responsible for mild to severe, life-threatening infections. GAS expresses a wide range of virulence factors, including the M family proteins. The M proteins allow the bacteria to evade parts of the human immune defenses by triggering the formation of a dense coat of plasma proteins surrounding the bacteria, including IgGs. However, the molecular level details of the M1-IgG interaction have remained unclear. Here, we characterized the structure and dynamics of this interaction interface in human plasma on the surface of live bacteria using integrative structural biology, combining cross-linking mass spectrometry and molecular dynamics (MD) simulations. We show that the primary interaction is formed between the S-domain of M1 and the conserved IgG Fc-domain. In addition, we show evidence for a so far uncharacterized interaction between the A-domain and the IgG Fc-domain. Both these interactions mimic the protein G-IgG interface of group C and G streptococcus. These findings underline a conserved scavenging mechanism used by GAS surface proteins that block the IgG-receptor (FcγR) to inhibit phagocytic killing. We additionally show that we can capture Fab-bound IgGs in a complex background and identify XLs between the constant region of the Fab-domain and certain regions of the M1 protein engaged in the Fab-mediated binding. Our results elucidate the M1-IgG interaction network involved in inhibition of phagocytosis and reveal important M1 peptides that can be further investigated as future vaccine targets. Streptococcus pyogenes is a human specific pathogen causing both mild and invasive infections. It employs sophisticated mechanisms to evade and circumvent parts of the host’s immune defenses, in part via its major surface associated virulence factor, the family of M proteins. Of these, the M1 protein is the most prevalent serotype. The M1 protein creates a dense coat-like structure with multiple host proteins on the bacterial surface to disguise itself from opsonizing antibodies. It specifically interacts in a non-immune way with human immunoglobulin G (IgG) Fc-domains to disarm their receptor binding site. The molecular level details of this interaction have not been characterized. Here, we describe these interactions from minimally perturbed samples of human plasma adsorbed onto living bacteria using an integrative structural biology approach including cross-linking mass spectrometry, molecular modeling, and molecular dynamics simulations. We identify two distinct M1-peptides that bind IgGs and reveal the stability of these interactions. We show that both peptides block the Fc-receptor binding sites through capturing IgGs via their Fc-domains. These results highlight the importance of describing novel pathogen-derived peptides mediating host immune evasion as potential vaccine targets in future studies.
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Giagulli C, Caccuri F, Zorzan S, Bugatti A, Zani A, Filippini F, Manocha E, D'Ursi P, Orro A, Dolcetti R, Caruso A. B-cell clonogenic activity of HIV-1 p17 variants is driven by PAR1-mediated EGF transactivation. Cancer Gene Ther 2020; 28:649-666. [PMID: 33093643 PMCID: PMC8203498 DOI: 10.1038/s41417-020-00246-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/30/2020] [Accepted: 10/08/2020] [Indexed: 11/29/2022]
Abstract
Combined antiretroviral therapy (cART) for HIV-1 dramatically slows disease progression among HIV+ individuals. Currently, lymphoma represents the main cause of death among HIV-1-infected patients. Detection of p17 variants (vp17s) endowed with B-cell clonogenic activity in HIV-1-seropositive patients with lymphoma suggests their possible role in lymphomagenesis. Here, we demonstrate that the clonogenic activity of vp17s is mediated by their binding to PAR1 and to PAR1-mediated EGFR transactivation through Gq protein. The entire vp17s-triggered clonogenic process is MMPs dependent. Moreover, phosphoproteomic and bioinformatic analysis highlighted the crucial role of EGFR/PI3K/Akt pathway in modulating several molecules promoting cancer progression, including RAC1, ABL1, p53, CDK1, NPM, Rb, PTP-1B, and STAT1. Finally, we show that a peptide (F1) corresponding to the vp17s functional epitope is sufficient to trigger the PAR1/EGFR/PI3K/Akt pathway and bind PAR1. Our findings suggest novel potential therapeutic targets to counteract vp17-driven lymphomagenesis in HIV+ patients.
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Affiliation(s)
- Cinzia Giagulli
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | - Francesca Caccuri
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | - Simone Zorzan
- Plantech, Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science & Technology (LIST), L-4422, Belvaux, Luxembourg
| | - Antonella Bugatti
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | - Alberto Zani
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | - Federica Filippini
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | - Ekta Manocha
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | - Pasqualina D'Ursi
- Department of Biomedical Sciences, Institute for Biomedical Technologies e National Research Council (ITB-CNR), 20090, Segrate (MI), Italy
| | - Alessandro Orro
- Department of Biomedical Sciences, Institute for Biomedical Technologies e National Research Council (ITB-CNR), 20090, Segrate (MI), Italy
| | - Riccardo Dolcetti
- University of Queensland Diamantina Institute, Translational Research Institute, University of Queensland, Brisbane, QLD, Australia.,Cancer Bio-Immunotherapy Unit, Centro di Riferimento Oncologico - IRCCS, Aviano, Italy
| | - Arnaldo Caruso
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy.
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9
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Wang X, Li Z, Ly N, Zhou F. One-Step Ligand Immobilization and Single Sample Injection for Regeneration-Free Surface Plasmon Resonance Measurements of Biomolecular Interactions. Anal Chem 2017; 89:3261-3265. [PMID: 28225259 DOI: 10.1021/acs.analchem.7b00121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Surface plasmon resonance (SPR) has been well established as a method of choice for label-free kinetic measurements of biomolecular interactions. The conventional approach involves multiple injections of an analyte of different concentrations into a fluidic channel covered with a fixed ligand density. Optimization of the experimental conditions and assessment of the data quality can be complicated by issues such as disruption of the ligand structure by the regeneration step and the limited availability of the sample solution. By sequentially closing fluidic channels on a five-channel SPR instrument, different densities of a ligand can be immobilized and determined in one step. With a subsequent injection of a single sample solution, SPR sensorgrams can be simultaneously collected to yield binding and dissociation rate constants (ka and kd) and dissociation constant (KD) between the ligand and analyte. For biomolecular interactions that obey the Langmuir isotherm, we show that the fidelity of the kinetic data can only be reliably confirmed when there exists a strong linear correlation between the SPR signals and the ligand densities. The use of a multichannel SPR instrument also obviates the regeneration step, allowing the binding kinetics between the green fluorescent protein and its antibody to be measured. In comparison to the conventional approach, the method simplifies the experimental procedure, reduces costs associated with sensor chips and biological samples, expedites kinetic measurements, and allows affinity constants to be determined more straightforwardly.
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Affiliation(s)
- Xiaoying Wang
- College of Chemistry and Chemical Engineering, Central South University , Changsha, Hunan, P. R. China , 410083.,Department of Chemistry and Biochemistry, California State University, Los Angeles , Los Angeles, California 90032, United States
| | - Zhiqiang Li
- College of Chemistry and Chemical Engineering, Central South University , Changsha, Hunan, P. R. China , 410083.,Department of Chemistry and Biochemistry, California State University, Los Angeles , Los Angeles, California 90032, United States
| | - Nguyen Ly
- Biosensing Instrument Inc. , Tempe, Arizona 85284, United States
| | - Feimeng Zhou
- Department of Chemistry and Biochemistry, California State University, Los Angeles , Los Angeles, California 90032, United States
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10
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Giorgio C, Russo S, Incerti M, Bugatti A, Vacondio F, Barocelli E, Mor M, Pala D, Hassan-Mohamed I, Gioiello A, Rusnati M, Lodola A, Tognolini M. Biochemical characterization of EphA2 antagonists with improved physico-chemical properties by cell-based assays and surface plasmon resonance analysis. Biochem Pharmacol 2015; 99:18-30. [PMID: 26462575 DOI: 10.1016/j.bcp.2015.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/06/2015] [Indexed: 12/28/2022]
Abstract
Amino acid conjugates of lithocholic acid (LCA) have been recently described as effective disruptors of the EphA2-ephrin-A1 interaction able to inhibit EphA2 phosphorylation in intact cells and thus able to block prometastatic responses such as cellular retraction and angiogenesis. However, these LCA-based compounds were significantly more potent at disrupting the EphA2-ephrin-A1 interaction than at blocking phenotype responses in cells, which might reflect an unclear mechanism of action or a metabolic issue responsible for a reduction of the compound concentration at the cell's surface. Through the synthesis of new compounds and their examination by a combination of cell-based assays and real-time interaction analysis by surface plasmon resonance, we showed at molecular level that l-tryptophan conjugates of lithocholic acid disrupt EphA2-ephrin-A1 interaction by targeting the EphA 2 receptor and that the presence of a polar group in position 3 of steroid scaffold is a key factor to increase the effective concentration of the compounds in cancer cell lines.
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Affiliation(s)
- Carmine Giorgio
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy
| | - Simonetta Russo
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy
| | - Matteo Incerti
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy
| | - Antonella Bugatti
- Dipartimento di Medicina Molecolare Traslazionale, Università degli Studi di Brescia, Brescia, Italy
| | - Federica Vacondio
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy
| | | | - Marco Mor
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy
| | - Daniele Pala
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy
| | | | - Antimo Gioiello
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Perugia, Italy
| | - Marco Rusnati
- Dipartimento di Medicina Molecolare Traslazionale, Università degli Studi di Brescia, Brescia, Italy
| | - Alessio Lodola
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy; Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, UK.
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11
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Di Noto G, Bugatti A, Zendrini A, Mazzoldi EL, Montanelli A, Caimi L, Rusnati M, Ricotta D, Bergese P. Merging colloidal nanoplasmonics and surface plasmon resonance spectroscopy for enhanced profiling of multiple myeloma-derived exosomes. Biosens Bioelectron 2015; 77:518-24. [PMID: 26469728 DOI: 10.1016/j.bios.2015.09.061] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/25/2015] [Accepted: 09/27/2015] [Indexed: 01/31/2023]
Abstract
A novel approach for sorting exosomes from multiple myeloma (MM), monoclonal gammopathy of undetermined significance (MGUS) and healthy individuals is presented. The method is based on the combination of colloidal gold nanoplasmonics and surface plasmon resonance (SPR) biosensing and probes distinctive colloidal properties of MM-derived exosomes, such as molar concentration and cell membrane binding preferences. It allowed to discover that MM patients produce about four folds more exosomes than MGUS and healthy individuals. In addition, it showed that among the analyzed exosomes, only the MM-derived ones bind heparin - a structural analog of heparan sulfate proteoglycans known to mediate exosome endocytosis - with an apparent dissociation constant (Kd) equal to about 1 nM, indicating a high affinity binding. This plasmonic method complements the classical biochemical profiling approach to exosomes, expanding the MM biomarker panel and adding biosensors to the toolbox to diagnose MM. It may find applications for other diseases and has wider interest for fundamental and translational research involving exosomes.
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Affiliation(s)
- Giuseppe Di Noto
- Department of Molecular and Translational Medicine and INSTM, University of Brescia, Viale Europa, 11, 25132 Brescia, Italy.
| | - Antonella Bugatti
- Department of Molecular and Translational Medicine and INSTM, University of Brescia, Viale Europa, 11, 25132 Brescia, Italy
| | - Andrea Zendrini
- Department of Molecular and Translational Medicine and INSTM, University of Brescia, Viale Europa, 11, 25132 Brescia, Italy
| | - Elena Laura Mazzoldi
- Department of Molecular and Translational Medicine and INSTM, University of Brescia, Viale Europa, 11, 25132 Brescia, Italy
| | - Alessandro Montanelli
- Spedali Civili of Brescia, Clinical Chemistry Laboratory, P.le Spedali Civili 1, 25123 Brescia, Italy
| | - Luigi Caimi
- Department of Molecular and Translational Medicine and INSTM, University of Brescia, Viale Europa, 11, 25132 Brescia, Italy
| | - Marco Rusnati
- Department of Molecular and Translational Medicine and INSTM, University of Brescia, Viale Europa, 11, 25132 Brescia, Italy
| | - Doris Ricotta
- Department of Molecular and Translational Medicine and INSTM, University of Brescia, Viale Europa, 11, 25132 Brescia, Italy
| | - Paolo Bergese
- Department of Molecular and Translational Medicine and INSTM, University of Brescia, Viale Europa, 11, 25132 Brescia, Italy.
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12
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Priya A, Kalaidzidis IV, Kalaidzidis Y, Lambright D, Datta S. Molecular Insights into Rab7-Mediated Endosomal Recruitment of Core Retromer: Deciphering the Role of Vps26 and Vps35. Traffic 2014; 16:68-84. [DOI: 10.1111/tra.12237] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 10/31/2014] [Accepted: 10/31/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Amulya Priya
- Department of Biological Sciences; Indian Institute of Science Education and Research Bhopal; ITI Gas Rahat Building Bhopal 462023 India
| | - Inna V Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics; 108 Pfotenhauerstrasse Dresden 01307 Germany
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics; 108 Pfotenhauerstrasse Dresden 01307 Germany
- Faculty of Bioengineering and Bioinformatics; Moscow State University; Moscow 119991 Russia
| | - David Lambright
- Program in Molecular Medicine; University of Massachusetts Medical School; 373 Plantation Street Worcester MA 01605 USA
| | - Sunando Datta
- Department of Biological Sciences; Indian Institute of Science Education and Research Bhopal; ITI Gas Rahat Building Bhopal 462023 India
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13
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MacGriff CA, Wang S, Tao N. Note: Four-port microfluidic flow-cell with instant sample switching. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:106110. [PMID: 24182183 PMCID: PMC4108724 DOI: 10.1063/1.4826359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 10/07/2013] [Indexed: 06/02/2023]
Abstract
A simple device for high-speed microfluidic delivery of liquid samples to a surface plasmon resonance sensor surface is presented. The delivery platform is comprised of a four-port microfluidic cell, two ports serve as inlets for buffer and sample solutions, respectively, and a high-speed selector valve to control the alternate opening and closing of the two outlet ports. The time scale of buffer/sample switching (or sample injection rise and fall time) is on the order of milliseconds, thereby minimizing the opportunity for sample plug dispersion. The high rates of mass transport to and from the central microfluidic sensing region allow for SPR-based kinetic analysis of binding events with dissociation rate constants (k(d)) up to 130 s(-1). The required sample volume is only 1 μL, allowing for minimal sample consumption during high-speed kinetic binding measurement.
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Affiliation(s)
- Christopher A MacGriff
- School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
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14
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A novel retro-inverso peptide is a preferential JNK substrate-competitive inhibitor. Int J Biochem Cell Biol 2013; 45:1939-50. [DOI: 10.1016/j.biocel.2013.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/04/2013] [Accepted: 06/11/2013] [Indexed: 12/22/2022]
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15
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Espiritu RA, Matsumori N, Murata M, Nishimura S, Kakeya H, Matsunaga S, Yoshida M. Interaction between the marine sponge cyclic peptide theonellamide A and sterols in lipid bilayers as viewed by surface plasmon resonance and solid-state (2)H nuclear magnetic resonance. Biochemistry 2013; 52:2410-8. [PMID: 23477347 DOI: 10.1021/bi4000854] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Theonellamides (TNMs) are members of a distinctive family of antifungal and cytotoxic bicyclic dodecapeptides isolated from the marine sponge Theonella sp. Recently, it has been shown that TNMs recognize 3β-hydroxysterol-containing membranes, induce glucan overproduction, and damage cellular membranes. However, to date, the detailed mode of sterol binding at a molecular level has not been determined. In this study, to gain insight into the mechanism of sterol recognition of TNM in lipid bilayers, surface plasmon resonance (SPR) experiments and solid-state deuterium nuclear magnetic resonance ((2)H NMR) measurements were performed on theonellamide A (TNM-A). SPR results revealed that the incorporation of 10 mol % cholesterol or ergosterol into 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes significantly enhances the affinity of the peptide for the membrane, particularly in the initial binding to the membrane surface. These findings, together with the fact that binding of TNM-A to epicholesterol (3α-cholesterol)-containing liposomes and pure POPC liposomes was comparably weak, confirmed the preference of the peptide for the 3β-hydroxysterol-containing membranes. To further establish the formation of the complex of TNM-A with 3β-hydroxysterols in lipid bilayers, solid-state (2)H NMR measurements were conducted using deuterium-labeled cholesterol, ergosterol, or epicholesterol. The (2)H NMR spectra showed that TNM-A significantly inhibits the fast rotational motion of cholesterol and ergosterol, but not epicholesterol, therefore verifying the direct complexation between TNM-A and 3β-hydroxysterols in lipid bilayers. This study demonstrates that TNM-A directly recognizes the 3β-OH moiety of sterols, which greatly facilitates its binding to bilayer membranes.
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Affiliation(s)
- Rafael Atillo Espiritu
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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16
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Matte A, Bertoldi M, Mohandas N, An X, Bugatti A, Brunati AM, Rusnati M, Tibaldi E, Siciliano A, Turrini F, Perrotta S, De Franceschi L. Membrane association of peroxiredoxin-2 in red cells is mediated by the N-terminal cytoplasmic domain of band 3. Free Radic Biol Med 2013; 55:27-35. [PMID: 23123411 DOI: 10.1016/j.freeradbiomed.2012.10.543] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 09/11/2012] [Accepted: 10/12/2012] [Indexed: 01/31/2023]
Abstract
Band 3 (B3), the anion transporter, is an integral membrane protein that plays a key structural role by anchoring the plasma membrane to the spectrin-based membrane skeleton in the red cell. In addition, it also plays a critical role in the assembly of glycolytic enzymes to regulate red cell metabolism. However, its ability to recruit proteins that can prevent membrane oxidation has not been previously explored. In this study, using a variety of experimental approaches including cross-linking studies, fluorescence and dichroic measurements, surface plasmon resonance analysis, and proteolytic digestion assays, we document that the antioxidant protein peroxiredoxin-2 (PRDX2), the third most abundant cytoplasmic protein in RBCs, interacts with the cytoplasmic domain of B3. The surface electrostatic potential analysis and stoichiometry measurements revealed that the N-terminal peptide of B3 is involved in the interaction. PRDX2 underwent a conformational change upon its binding to B3 without losing its peroxidase activity. Hemichrome formation induced by phenylhydrazine of RBCs prevented membrane association of PRDX2, implying overlapping binding sites. Documentation of the absence of binding of PRDX2 to B3 Neapolis red cell membranes, in which the initial N-terminal 11 amino acids are deleted, enabled us to conclude that PRDX2 binds to the N-terminal cytoplasmic domain of B3 and that the first 11 amino acids of this domain are crucial for PRDX2 membrane association in intact RBCs. These findings imply yet another important role for B3 in regulating red cell membrane function.
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Affiliation(s)
- Alessandro Matte
- Section of Internal Medicine, Department of Medicine,University of Verona, 37134 Verona, Italy
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17
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Bugatti A, Giagulli C, Urbinati C, Caccuri F, Chiodelli P, Oreste P, Fiorentini S, Orro A, Milanesi L, D'Ursi P, Caruso A, Rusnati M. Molecular interaction studies of HIV-1 matrix protein p17 and heparin: identification of the heparin-binding motif of p17 as a target for the development of multitarget antagonists. J Biol Chem 2012; 288:1150-61. [PMID: 23166320 DOI: 10.1074/jbc.m112.400077] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Once released by HIV(+) cells, p17 binds heparan sulfate proteoglycans (HSPGs) and CXCR1 on leukocytes causing their dysfunction. By exploiting an approach integrating computational modeling, site-directed mutagenesis of p17, chemical desulfation of heparin, and surface plasmon resonance, we characterized the interaction of p17 with heparin, a HSPG structural analog, and CXCR1. p17 binds to heparin with an affinity (K(d) = 190 nm) that is similar to those of other heparin-binding viral proteins. Two stretches of basic amino acids (basic motifs) are present in p17 N and C termini. Neutralization (Arg→Ala substitution) of the N-terminal, but not of the C-terminal basic motif, causes the loss of p17 heparin-binding capacity. The N-terminal heparin-binding motif of p17 partially overlaps the CXCR1-binding domain. Accordingly, its neutralization prevents also p17 binding to the chemochine receptor. Competition experiments demonstrated that free heparin and heparan sulfate (HS), but not selectively 2-O-, 6-O-, and N-O desulfated heparins, prevent p17 binding to substrate-immobilized heparin, indicating that the sulfate groups of the glycosaminoglycan mediate p17 interaction. Evaluation of the p17 antagonist activity of a panel of biotechnological heparins derived by chemical sulfation of the Escherichia coli K5 polysaccharide revealed that the highly N,O-sulfated derivative prevents the binding of p17 to both heparin and CXCR1, thus inhibiting p17-driven chemotactic migration of human monocytes with an efficiency that is higher than those of heparin and HS. Here, we characterized at a molecular level the interaction of p17 with its cellular receptors, laying the basis for the development of heparin-mimicking p17 antagonists.
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Affiliation(s)
- Antonella Bugatti
- Section of Experimental Oncology and Immunology, School of Medicine, University of Brescia, Brescia 25123, Italy
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18
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Marchiò S, Soster M, Cardaci S, Muratore A, Bartolini A, Barone V, Ribero D, Monti M, Bovino P, Sun J, Giavazzi R, Asioli S, Cassoni P, Capussotti L, Pucci P, Bugatti A, Rusnati M, Pasqualini R, Arap W, Bussolino F. A complex of α6 integrin and E-cadherin drives liver metastasis of colorectal cancer cells through hepatic angiopoietin-like 6. EMBO Mol Med 2012; 4:1156-75. [PMID: 23070965 PMCID: PMC3494873 DOI: 10.1002/emmm.201101164] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 09/04/2012] [Accepted: 09/07/2012] [Indexed: 01/09/2023] Open
Abstract
Homing of colorectal cancer (CRC) cells to the liver is a non-random process driven by a crosstalk between tumour cells and components of the host tissue. Here we report the isolation of a liver metastasis-specific peptide ligand (CGIYRLRSC) that binds a complex of E-cadherin and α(6) integrin on the surface of CRC cells. We identify angiopoietin-like 6 protein as a peptide-mimicked natural ligand enriched in hepatic blood vessels of CRC patients. We demonstrate that an interaction between hepatic angiopoietin-like 6 and tumoural α(6) integrin/E-cadherin drives liver homing and colonization by CRC cells, and that CGIYRLRSC inhibits liver metastasis through interference with this ligand/receptor system. Our results indicate a mechanism for metastasis whereby a soluble factor accumulated in normal vessels functions as a specific ligand for circulating cancer cells. Consistently, we show that high amounts of coexpressed α(6) integrin and E-cadherin in primary tumours represent a poor prognostic factor for patients with advanced CRC.
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Affiliation(s)
- Serena Marchiò
- Department of Oncology, University of Turin, Candiolo, Italy.
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19
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HIV-1 matrix protein p17 binds to the IL-8 receptor CXCR1 and shows IL-8–like chemokine activity on monocytes through Rho/ROCK activation. Blood 2012; 119:2274-83. [DOI: 10.1182/blood-2011-06-364083] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
AbstractExogenous HIV-1 matrix protein p17 was found to deregulate biologic activities of many different immune cells that are directly or indirectly involved in AIDS pathogenesis after binding to unknown cellular receptor(s). In particular, p17 was found to induce a functional program in monocytes related to activation and inflammation. In the present study, we demonstrate that CXCR1 is the receptor molecule responsible for p17 chemokine–like activity on monocytes. After CXCR1 binding, p17 was capable of triggering rapid adhesion and chemotaxis of monocytes through a pathway that involved Rho/ROCK. Moreover, CXCR1-silenced primary monocytes lost responsiveness to p17 chemoattraction, whereas CXCR1-transfected Jurkat cells acquired responsiveness. Surface plasmon resonance studies confirmed the capacity of p17 to bind CXCR1 and showed that the p17/CXCR1 interaction occurred with a low affinity compared with that measured for IL-8, the physiologic CXCR1 ligand. In all of its activities, p17 mimicked IL-8, the natural high-affinity ligand of CXCR1. Recent studies have highlighted the role of IL-8 and CXCR1 in HIV-1 replication and AIDS pathogenesis. Our findings herein call for an exploration of the therapeutic potential of blocking the p17/IL-8/CXCR1 axis in HIV-1 infection.
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20
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Ghosh T, Williams L, Mastrangelo CH. Label-free detection of protein binding with multisine SPR microchips. LAB ON A CHIP 2011; 11:4194-9. [PMID: 22033816 DOI: 10.1039/c1lc20260j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Label-free techniques such as surface plasmon resonance (SPR) have used a step-response excitation method to characterize the binding of two biochemical entities. A major drawback of the step response technique is its high susceptibility to thermal drifts and noise which directly determine the minimum detectable binding mass. In this paper we present a new frequency-domain method based on the use of multisine chemical excitation that is much less sensitive to these disturbances. The multisine method was implemented in a PDMS microfluidic chip using a dual channel, dual multiplug chemical signal generator connected to functionalized and reference SPR binding spots. Kinetic constants for the reaction are extracted from the characteristics of the sense spot response versus frequency. The feasibility of the technique was tested using a model system of Carbonic Anhydrase-II analyte and amino-benzenesulfonamide ligand. The experimental signal to noise ratio (SNR) for the multisine measurement is about 32 dB; 7 dB higher than that observed with the single step-response method, while the overall measurement time is twice as long as the step method.
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Affiliation(s)
- Tridib Ghosh
- Department of Bioengineering, University of Utah, Salt Lake City, UT, USA.
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21
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Abstract
An improved understanding of the roles of protein kinases in intracellular signalling and disease progression has driven significant advances in protein kinase inhibitor discovery. Peptide inhibitors that target the kinase protein substrate-binding site have continued to attract attention. In the present paper, we describe a novel JNK (c-Jun N-terminal kinase) inhibitory peptide PYC71N, which inhibits JNK activity in vitro towards a range of recombinant protein substrates including the transcription factors c-Jun, ATF2 (activating trancription factor 2) and Elk1, and the microtubule regulatory protein DCX (doublecortin). Analysis of cell culture studies confirmed the actions of a cell-permeable version of PYC71 to inhibit c-Jun phosphorylation during acute hyperosmotic stress. The analysis of the in vitro data for the kinetics of this inhibition indicated a substrate–inhibitor complex-mediated inhibition of JNK by PYC71N. Alanine-scanning replacement studies revealed the importance of two residues (PYC71N Phe9 or Phe11 within an FXF motif) for JNK inhibition. The importance of these residues was confirmed through interaction studies showing that each change decreased interaction of the peptide with c-Jun. Furthermore, PYC71N interacted with both non-phosphorylated (inactive) JNK1 and the substrate c-Jun, but did not recognize active JNK1. In contrast, a previously characterized JNK-inhibitory peptide TIJIP [truncated inhibitory region of JIP (JNK-interacting protein)], showed stronger interaction with active JNK1. Competition binding analysis confirmed that PYC71N inhibited the interaction of c-Jun with JNK1. Taken together, the results of the present study define novel properties of the PYC71N peptide as well as differences from the characterized TIJIP, and highlight the value of these peptides to probe the biochemistry of JNK-mediated substrate interactions and phosphorylation.
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22
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Williams LD, Ghosh T, Mastrangelo CH. Low noise detection of biomolecular interactions with signal-locking surface plasmon resonance. Anal Chem 2010; 82:6025-31. [PMID: 20568712 DOI: 10.1021/ac100504b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Surface plasmon resonance (SPR) is a popular technique for label-free detection of biomolecular interactions at a surface. SPR yields quantitative kinetic association and dissociation constants of surface interactions such as the binding of two molecular species, one present in the liquid phase and the other immobilized at the surface. Current state-of-the-art SPR systems extract kinetic constants from measurements of the step response of the interaction versus time. The step response measurement is subject to the influence of noise and drift disturbances that limit its minimum-detectable mass changes. This paper presents a new SPR technique that measures the biomolecular interaction not in time but over a very narrow frequency range under periodic excitation. The measured response is, thus, locked to a very specific narrow band signal. This narrow band spectral sensing scheme has a very high degree of rejection to uncorrelated spurious signals. The signal-locked SPR technique was implemented using a chemical modulator chip connected to a set of functionalized Au sensing sites downstream. Binding experiments for a model system of carbonic anhydrase-II (CA-II) analyte and immobilized 4-(2-aminoethyl)benzenesulfonamide (ABS) ligand display a 100-fold (20 dB) improvement in the measured signal-to-noise ratio (SNR) when using the new technique compared to the SNR achieved using the conventional step response method.
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Affiliation(s)
- Layne D Williams
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, USA
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23
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Luppa PB, Metzger J, Schneider H. Surface plasmon resonance biosensorics in urine proteomics. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2010; 641:193-221. [PMID: 20407949 DOI: 10.1007/978-1-60761-711-2_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Surface plasmon resonance (SPR) is a novel biophysical detection method. In combination with sophisticated surface chemistries and sensing instrumentations, SPR biosensors are approved as tools for molecular interaction studies. SPR plays also a role in interaction proteomics. Once being detected in urine, SPR helps to unravel the functions of new proteins. Due to its outstanding analytical characteristics, SPR also moves more and more into the realm of quantitative analyses in the clinical laboratory. Complex urine determinations of proteins and/or metabolites will bring the SPR biosensor both to the core lab and to point-of-care-testing.This review delineates first the optical phenomena of SPR near to the gold surface, and also the main features of bioconjugation chemistry on a solid-state surface. Then the kinetic calculation of molecular interaction analysis using SPR is introduced. In order to portray the capability of the method, new applications in urine proteomics and proteinuria diagnostics are finally described in detail.
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Affiliation(s)
- Peter B Luppa
- Institut für Klinische Chemie, Krankenhaus München Rechts der Isar, München, Germany
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24
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Krishnamoorthy G, Carlen ET, Beusink JB, Schasfoort RBM, van den Berg A. Single injection microarray-based biosensor kinetics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2009; 1:162-169. [PMID: 32938053 DOI: 10.1039/b9ay00176j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Binding affinity of biomolecular interactions can be directly extracted from measured surface plasmon resonance biosensor sensorgrams by fitting the data to the appropriate model equations. The conventional method for affinity estimation uses a series of analytes and buffers that are injected serially to a single immobilized ligand on the sensing surface, including a regeneration step between each injection, to generate information about the binding behavior. We present an alternative method to estimate the affinity using a single analyte concentration injected to multiple ligand densities in a microarray format. This parameter estimation method eliminates the need for multiple analyte injections and surface regeneration steps, which can be important for applications where there is limited analyte serum, fragile ligand-surface attachment, or the detection of multiple biomolecule interactions. The single analyte injection approach for binding affinity estimation has been demonstrated for two different interactant pairs, β2 microglobulin/anti-β2 microglobulin (β2M) and human IgG/Fab fragments of anti-human IgG (hIgG), where the ligands are printed in a microarray format. Quantitative comparisons between the estimated binding affinities measured with the conventional method are β2M: KD = 1.48 ± 0.28 nM and hIgG: KD = 12.6 ± 0.2 nM and for the single injection method are β2M: KD = 1.52 ± 0.22 nM and hIgG: KD = 12.5 ± 0.6 nM, which are in good agreement in both cases.
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Affiliation(s)
- Ganeshram Krishnamoorthy
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE Enschede, The Netherlands.
| | - Edwin T Carlen
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE Enschede, The Netherlands.
| | - J Bianca Beusink
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE Enschede, The Netherlands.
| | - Richard B M Schasfoort
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE Enschede, The Netherlands.
| | - Albert van den Berg
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE Enschede, The Netherlands.
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25
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Hernandez FJ, Kalra N, Wengel J, Vester B. Aptamers as a model for functional evaluation of LNA and 2'-amino LNA. Bioorg Med Chem Lett 2009; 19:6585-7. [PMID: 19864131 DOI: 10.1016/j.bmcl.2009.10.039] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 10/06/2009] [Accepted: 10/07/2009] [Indexed: 10/20/2022]
Abstract
The affinity change upon incorporation of LNA and 2'-amino-LNA monomers into an avidin binding DNA aptamer is described. The kinetic profile of selected modified-aptamer was obtained by surface plasmon resonance experiments and compared with the profile of the parent unmodified DNA aptamer. We report significant improvement of avidin binding affinity by the incorporation of single LNA modifications into the aptamer, and successful incorporation of 2'-amino LNA as a novel monomer in aptamers with potential function as carrier unit for additional molecular entities.
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Affiliation(s)
- Frank J Hernandez
- Biochemistry and Molecular Biology Department, Nucleic Acid Center, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
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26
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De Crescenzo G, Boucher C, Durocher Y, Jolicoeur M. Kinetic Characterization by Surface Plasmon Resonance-Based Biosensors: Principle and Emerging Trends. Cell Mol Bioeng 2008. [DOI: 10.1007/s12195-008-0035-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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27
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De Crescenzo G, Woodward L, Srinivasan B. Online optimization of surface plasmon resonance‐based biosensor experiments for improved throughput and confidence. J Mol Recognit 2008; 21:256-66. [DOI: 10.1002/jmr.894] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Binding kinetics of darunavir to human immunodeficiency virus type 1 protease explain the potent antiviral activity and high genetic barrier. J Virol 2007; 81:13845-51. [PMID: 17928344 DOI: 10.1128/jvi.01184-07] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The high incidence of cross-resistance between human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) limits their sequential use. This necessitates the development of PIs with a high genetic barrier and a broad spectrum of activity against PI-resistant HIV, such as tipranavir and darunavir (TMC114). We performed a surface plasmon resonance-based kinetic study to investigate the impact of PI resistance-associated mutations on the protease binding of five PIs used clinically: amprenavir, atazanavir, darunavir, lopinavir, and tipranavir. With wild-type protease, the binding affinity of darunavir was more than 100-fold higher than with the other PIs, due to a very slow dissociation rate. Consequently, the dissociative half-life of darunavir was much higher (>240 h) than that of the other PIs, including darunavir's structural analogue amprenavir. The influence of protease mutations on the binding kinetics was tested with five multidrug-resistant (MDR) proteases derived from clinical isolates harboring 10 to 14 PI resistance-associated mutations with a decreased susceptibility to various PIs. In general, all PIs bound to the MDR proteases with lower binding affinities, caused mainly by a faster dissociation rate. For amprenavir, atazanavir, lopinavir, and tipranavir, the decrease in affinity with MDR proteases resulted in reduced antiviral activity. For darunavir, however, a nearly 1,000-fold decrease in binding affinity did not translate into a weaker antiviral activity; a further decrease in affinity was required for the reduced antiviral effect. These observations provide a mechanistic explanation for darunavir's potent antiviral activity and high genetic barrier to the development of resistance.
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29
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Margosio B, Rusnati M, Bonezzi K, Cordes BLA, Annis DS, Urbinati C, Giavazzi R, Presta M, Ribatti D, Mosher DF, Taraboletti G. Fibroblast growth factor-2 binding to the thrombospondin-1 type III repeats, a novel antiangiogenic domain. Int J Biochem Cell Biol 2007; 40:700-9. [PMID: 17996481 DOI: 10.1016/j.biocel.2007.10.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 10/01/2007] [Accepted: 10/02/2007] [Indexed: 02/02/2023]
Abstract
Thrombospondin-1, an antiangiogenic matricellular protein, binds with high affinity to the angiogenic fibroblast growth factor-2, affecting its bioavailability and activity. The present work aimed at further locating the fibroblast growth factor-2 binding site of thrombospondin-1 and investigating its activity, using recombinant thrombospondin-1 proteins. Only recombinant constructs containing the thrombospondin-1 type III repeats bound fibroblast growth factor-2, whereas other domains, including the known anti-angiogenic type I repeats, were inactive. Binding was specific and inhibited by the anti thrombospondin-1 monoclonal antibody B5.2. Surface plasmon resonance analysis on BIAcore revealed a binding affinity (K(d)) of 310nM for the type III repeats and 11nM for intact thrombospondin-1. Since the type III repeats bind calcium, the effect of calcium on thrombospondin-1 binding to fibroblast growth factor-2 was investigated. Binding was modulated by calcium, as thrombospondin-1 or the type III repeats bound to fibroblast growth factor-2 only in calcium concentrations <0.3mM. The type III repeats inhibited binding of fibroblast growth factor-2 to endothelial cells, fibroblast growth factor-2-induced endothelial cell proliferation in vitro and angiogenesis in the chorioallantoic membrane assay in vivo, thus indicating the antiangiogenic activity of the domain. In conclusion, this study demonstrates that the fibroblast growth factor-2 binding site of thrombospondin-1 is located in the type III repeats. The finding that this domain is active in inhibiting angiogenesis indicates that the type III repeats represent a novel antiangiogenic domain of thrombospondin-1.
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Affiliation(s)
- Barbara Margosio
- Department of Oncology, Mario Negri Institute for Pharmacological Research, Bergamo, Italy
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30
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Hrtska SCL, Kemp MM, Muñoz EM, Azizad O, Banerjee M, Raposo C, Kumaran J, Ghosh P, Linhardt RJ. Investigation of the mechanism of binding between internalin B and heparin using surface plasmon resonance. Biochemistry 2007; 46:2697-706. [PMID: 17305366 PMCID: PMC2034450 DOI: 10.1021/bi062021x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Listeria monocytogenes, a food-borne pathogen that infects immunocompromised patients, enters and proliferates within mammalian cells by taking advantage of host cell machinery. While entry into macrophages and other phagocytic cells occurs constitutively, intracellular invasion of nonphagocytic cells, such as epithelial and endothelial cells, occurs through induced phagocytosis. Invasion of these nonphagocytic cell types is under the control of the secreted L. monocytogenes protein internalin B (InlB), which directly associates with and activates the receptor tyrosine kinase Met. Activation of Met by InlB has previously been shown to be potentiated by binding of glycosaminoglycans to the GW domains of this protein. We studied the interaction between heparin and full-length InlB as well as a truncated, functional form of InlB to understand the mode of interaction between these two molecules. InlB preferred long-chain (>or=dp14) heparin oligosaccharides, and the interaction with heparin fit a complicated binding model with a dissociation constant in the nanomolar range. While there are various explanations for this complicated binding model, one supported by our data involves binding and rebinding of InlB to multiple binding sites on heparin in a positive and weakly cooperative manner. This mode is consistent with enhancement of interaction of InlB with glycosaminoglycans for activation of Met.
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Affiliation(s)
- Sybil C Lang Hrtska
- Department of Chemical and Biochemical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
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31
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Balzarini J, Van Laethem K, Daelemans D, Hatse S, Bugatti A, Rusnati M, Igarashi Y, Oki T, Schols D. Pradimicin A, a carbohydrate-binding nonpeptidic lead compound for treatment of infections with viruses with highly glycosylated envelopes, such as human immunodeficiency virus. J Virol 2006; 81:362-73. [PMID: 17050611 PMCID: PMC1797273 DOI: 10.1128/jvi.01404-06] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pradimicin A (PRM-A), an antifungal nonpeptidic benzonaphtacenequinone antibiotic, is a low-molecular-weight (molecular weight, 838) carbohydrate binding agent (CBA) endowed with a selective inhibitory activity against human immunodeficiency virus (HIV). It invariably inhibits representative virus strains of a variety of HIV-1 clades with X4 and R5 tropisms at nontoxic concentrations. Time-of-addition studies revealed that PRM-A acts as a true virus entry inhibitor. PRM-A specifically interacts with HIV-1 gp120 and efficiently prevents virus transmission in cocultures of HUT-78/HIV-1 and Sup T1 cells. Upon prolonged exposure of HIV-1-infected CEM cell cultures, PRM-A drug pressure selects for mutant HIV-1 strains containing N-glycosylation site deletions in gp120 but not gp41. A relatively long exposure time to PRM-A is required before drug-resistant virus strains emerge. PRM-A has a high genetic barrier, since more than five N-glycosylation site deletions in gp120 are required to afford moderate drug resistance. Such mutated virus strains keep full sensitivity to the other known clinically used anti-HIV drugs. PRM-A represents the first prototype compound of a nonpeptidic CBA lead and, together with peptide-based lectins, belongs to a conceptually novel type of potential therapeutics for which drug pressure results in the selection of glycan deletions in the HIV gp120 envelope.
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Affiliation(s)
- Jan Balzarini
- Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
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Rosenbluh J, Kapelnikov A, Shalev DE, Rusnati M, Bugatti A, Loyter A. Positively charged peptides can interact with each other, as revealed by solid phase binding assays. Anal Biochem 2006; 352:157-68. [PMID: 16581010 DOI: 10.1016/j.ab.2006.03.002] [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: 10/09/2005] [Revised: 12/19/2005] [Accepted: 03/01/2006] [Indexed: 11/24/2022]
Abstract
Solid phase assay systems such as enzyme-linked immunosorbent assay (ELISA), surface plasmon resonance (SPR), and overlay gels are used to study processes of protein-protein interactions. The common principle of all these methods is that they monitor the binding between soluble and surface-immobilized molecules. Following the use of bovine serum albumin (BSA)-peptide conjugates or isolated synthetic peptides and the above-mentioned solid phase assay systems, the results of the current work demonstrate that positively charged peptides can interact with each other. Both the ELISA and SPR methods demonstrated that the binding process reached saturation with K(d) values ranging between 1 and 14 nM. No interaction was observed between BSA conjugates bearing positively charged peptides and conjugates bearing negatively charged peptides or with pure BSA molecules, strengthening the view that interaction occurs only between positively charged peptides. However, interactions between peptides in solution were not observed by nuclear magnetic resonance (NMR) or by native gel electrophoresis. It appears that for positively charged molecules to interact, one of the binding partners must be immobilized to a surface, a process that may lead to the exposure of otherwise masked groups or atoms. We discuss the relevance of our findings for the use of solid phase assay systems to study interactions between biomolecules.
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Affiliation(s)
- Joseph Rosenbluh
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel
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Nakajima H, Cocquerel L, Kiyokawa N, Fujimoto J, Levy S. Kinetics of HCV envelope proteins' interaction with CD81 large extracellular loop. Biochem Biophys Res Commun 2005; 328:1091-100. [PMID: 15707989 DOI: 10.1016/j.bbrc.2005.01.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Indexed: 10/25/2022]
Abstract
We used BIAcore to analyze the kinetics of interactions between CD81 and hepatitis C virus (HCV) envelope proteins. We immobilized different forms of HCV envelope proteins (E1E2, E2, and E2(661)) on the sensor and monitored their interaction with injected fusion proteins of CD81 large extracellular loop (CD81LEL) and glutathione-S-transferase (CD81LEL-GST) or maltose binding protein (CD81LEL-MBP). The difference between the GST and MBP fusion proteins was their multimeric and monomeric forms, respectively. The association rate constants between CD81LEL-GST or CD81LEL-MBP and the E1E2, E2 or E2(661) HCV envelope proteins were similar. However, the dissociation rate constants of CD81LEL-MBP were higher than those of CD81LEL-GST. Interestingly, the dissociation rate constant of CD81LEL-GST from E1E2 was much lower than from E2 or E2(661). The interaction between both forms of the CD81LEL fusion proteins and the HCV envelope proteins best-fitted the "heterogeneous ligand" model. This model implies that two kinds of interactions occur between envelope proteins and CD81LEL: one is strong, the other is weak. It also implies that the heterogeneity is likely due to the HCV envelope proteins, which are known to form non-covalently linked heterodimers and disulfide-linked aggregate.
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Affiliation(s)
- Hideki Nakajima
- Division of Oncology, Department of Medicine, Stanford University Medical Center, Stanford, CA, USA
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Li Y, Moysey R, Molloy PE, Vuidepot AL, Mahon T, Baston E, Dunn S, Liddy N, Jacob J, Jakobsen BK, Boulter JM. Directed evolution of human T-cell receptors with picomolar affinities by phage display. Nat Biotechnol 2005; 23:349-54. [PMID: 15723046 DOI: 10.1038/nbt1070] [Citation(s) in RCA: 318] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Accepted: 12/16/2004] [Indexed: 01/22/2023]
Abstract
Peptides derived from almost all proteins, including disease-associated proteins, can be presented on the cell surface as peptide-human leukocyte antigen (pHLA) complexes. T cells specifically recognize pHLA with their clonally rearranged T-cell receptors (TCRs), whose natural affinities are limited to approximately 1-100 muM. Here we describe the display of ten different human TCRs on the surface of bacteriophage, stabilized by a nonnative interchain disulfide bond. We report the directed evolution of high-affinity TCRs specific for two different pHLAs: the human T-cell lymphotropic virus type 1 (HTLV-1) tax(11-19) peptide-HLA-A(*)0201 complex and the NY-ESO-1(157-165) tumor-associated peptide antigen-HLA-A(*)0201 complex, with affinities of up to 2.5 nM and 26 pM, respectively, and we demonstrate their high specificity and sensitivity for targeting of cell-surface pHLAs.
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Onell A, Andersson K. Kinetic determinations of molecular interactions using Biacore—minimum data requirements for efficient experimental design. J Mol Recognit 2005; 18:307-17. [PMID: 15952219 DOI: 10.1002/jmr.745] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Reliable kinetic estimates can be obtained from significantly less data than is commonly used today, particularly in the characterization of 1:1 interactions involving low molecular weight compounds and proteins. We have designed a rational and cost-effective strategy to determine kinetic constants using Biacore's surface plasmon resonance-based biosensors and show that the number of measurements necessary for accurate kinetic determinations can be greatly reduced, increasing sample throughput and saving sample material. Simulated and measured data for a range of possible 1:1 interactants were studied to find the minimum requirements of a data set for kinetic analysis. The results showed that kinetic constants in the region 10(4) < k(a) < 10(7) M(-1) s(-1) (association) and 10(-4) < k(d) < 10(-1) s(-1) (dissociation) could easily be determined in a 1:1 interaction model. Owing to the information-dense nature of Biacore data, only two sample concentrations were necessary to reliably determine the kinetics. A standard sample concentration series consisting of 10-fold dilutions between approximately 10 microM and approximately 1 nM consistently provided at least two concentrations with sufficient information about the interaction in this region. Determinations of the constants became increasingly unreliable outside this region. If the rate constants prove to be outside the specified region or the data fits poorly to the 1:1-MTL model, more experiments are required. General recommendations for the design of a cost-effective assay to deliver reliable kinetic measurements are provided.
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Jenkins J, Prabhakarpandian B, Lenghaus K, Hickman J, Sundaram S. Fluidics-resolved estimation of protein adsorption kinetics in a biomicrofluidic system. Anal Biochem 2004; 331:207-15. [PMID: 15265724 DOI: 10.1016/j.ab.2004.03.072] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2003] [Indexed: 10/26/2022]
Abstract
Protein adsorption on surfaces is a complex phenomenon that is described by the balance of convective/diffusive transport of the protein species to the surface and its adsorption/desorption at the surface. The extent of binding depends on a variety of factors such as protein/surface interactions, availability of binding sites, localized concentrations of protein near biomaterial surfaces and flow characteristics of the protein in that region. Factors such as time-varying flows, complex device geometries, presence of multiple competitive species, or possible denaturing of proteins when they attach to the surface make it extremely difficult to quantitatively analyze protein interactions with surfaces. Adsorption/desorption rate constants are often inferred using simplistic models which neglect mass transport and have limited use across different microfluidic systems and flow protocols. In this work, we have developed and demonstrated a fluidics-resolved model that evaluates protein adsorption, accounting for both the fluidic transport and the biochemical kinetics in complex biomicrofluidic devices. The model is valid for both flow and static conditions. An automated procedure was also developed to extract the "intrinsic" mass-transport-independent adsorption kinetic rate constants from experimental data using a least squares optimization method. The automated data extraction methodology is applied to two proteins (alkaline phosphatase and glucose oxidase) that have been brought into contact with poly(etheretherketone) and Teflon capillaries. The applicability of the procedure in analyzing flow and adsorption in complex microfluidic structures is also demonstrated.
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Affiliation(s)
- J Jenkins
- CFD Research Corp. Huntsville, AL 35805, USA
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Urbinati C, Bugatti A, Oreste P, Zoppetti G, Waltenberger J, Mitola S, Ribatti D, Presta M, Rusnati M. Chemically sulfatedEscherichia coliK5 polysaccharide derivatives as extracellular HIV-1 Tat protein antagonists. FEBS Lett 2004; 568:171-7. [PMID: 15196942 DOI: 10.1016/j.febslet.2004.05.033] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2004] [Revised: 05/13/2004] [Accepted: 05/19/2004] [Indexed: 10/26/2022]
Abstract
The HIV-1 transactivating factor (Tat) acts as an extracellular cytokine on target cells, including endothelium. Here, we report about the Tat-antagonist capacity of chemically sulfated derivatives of the Escherichia coli K5 polysaccharide. O-sulfated K5 with high sulfation degree (K5-OS(H)) and N,O-sulfated K5 with high (K5-N,OS(H)) or low (K5-N,OS(L)) sulfation degree, but not unmodified K5, N-sulfated K5, and O-sulfated K5 with low sulfation degree, bind to Tat preventing its interaction with cell surface heparan sulfate proteoglycans, cell internalization, and consequent HIV-LTR-transactivation. Also, K5-OS(H) and K5-N,OS(H) prevent the interaction of Tat to the vascular endothelial growth factor receptor-2 on endothelial cell (EC) surface. Finally, K5-OS(H) inhibits alphav beta3 integrin/Tat interaction and EC adhesion to immobilized Tat. Consequently, K5-OS(H) and K5-N,OS(H) inhibit the angiogenic activity of Tat in vivo. In conclusion, K5 derivatives with distinct sulfation patterns bind extracellular Tat and modulate its interaction with cell surface receptors and affect its biological activities. These findings provide the basis for the design of novel extracellular Tat antagonists with possible implications in anti-AIDS therapies.
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Affiliation(s)
- Chiara Urbinati
- Unit of General Pathology and Immunology, Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, viale Europa 11, 25123 Brescia, Italy
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Abstract
We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Weidenhaupt M, Khalifa MB, Hugo N, Choulier L, Altschuh D, Vernet T. Functional mapping of conserved, surface-exposed charges of antibody variable domains. J Mol Recognit 2002; 15:94-103. [PMID: 11954054 DOI: 10.1002/jmr.562] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Surface-exposed charges can affect protein structure, stability and solubility as well as the kinetics of both the folding process and interaction with binding partners. We have investigated the influence on kinetic interaction parameters of 14 conserved, surface-exposed charges located away from the paratope in the variable domains of two antibodies of different specificity. We found that conserved, surface-exposed, charged framework residues are asymmetrically distributed on opposite faces of both VH and VL domains. Some of the charges play a critical role in protein folding and stability. While electrostatic forces within or close to the binding interface can be used to optimize the association rate, we confirmed the predicted minor effects of charge modifications remote from the binding site. They had no effect on the dissociation rate parameter. Our study demonstrates the role of residues remote from the interaction site in the recognition function as well as the limited effect of surface charge modifications in antibody fragments on kinetic interaction parameters.
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Affiliation(s)
- Marianne Weidenhaupt
- Institut de Biologie Structurale Jean-Pierre Ebel, Laboratoire d'Ingénierie des Macromolécules, CEA/CNRS/UJF, 41 rue Jules Horowitz,-F-38027 Grenoble cedex 1, France
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