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Abstract
Superantigens are unconventional antigens which recognise immune receptors outside their usual recognition sites e.g. complementary determining regions (CDRs), to elicit a response within the target cell. T-cell superantigens crosslink T-cell receptors and MHC Class II molecules on antigen-presenting cells, leading to lymphocyte recruitment, induction of cytokine storms and T-cell anergy or apoptosis among many other effects. B-cell superantigens, on the other hand, bind immunoglobulins on B-cells, affecting opsonisation, IgG-mediated phagocytosis, and driving apoptosis. Here, through a review of the structural basis for recognition of immune receptors by superantigens, we show that their binding interfaces share specific physicochemical characteristics when compared with other protein-protein interaction complexes. Given that antibody-binding superantigens have been exploited extensively in industrial antibody purification, these observations could facilitate further protein engineering to optimize the use of superantigens in this and other areas of biotechnology.
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Affiliation(s)
- Anthony M. Deacy
- School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, United Kingdom
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Experimental Drug Development Centre – Bioinformatics Institute (EDDC-BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore
- James Cook University, Singapore, Singapore
| | - Jeremy P. Derrick
- School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, United Kingdom
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2
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Kim SJ, Dixon AS, Adamovich PC, Robinson PD, Owen SC. Homogeneous Immunoassay Using a Tri-Part Split-Luciferase for Rapid Quantification of Anti-TNF Therapeutic Antibodies. ACS Sens 2021; 6:1807-1814. [PMID: 34010570 DOI: 10.1021/acssensors.0c02642] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Anti-TNF therapeutics bind and sequester tumor necrosis factor (TNF) to prevent downstream signaling and are clinically important in the treatment of several autoimmune diseases. Effective treatment with these drugs requires frequent therapeutic drug monitoring (TDM). Current analytical methods, including reporter gene assay (RGA), enzyme-linked immunosorbent assay (ELISA), and mobility shift assay (MSA), can be technically rigorous, slow, and expensive. These qualities prevent the implementation of point-of-care testing and ultimately limit the frequency and utility of monitoring. An assay simple enough to be performed in the clinic would enable increased TDM frequency, more accurate dosing, and improved patient outcomes. Toward this end, we developed a homogeneous immunoassay based on a tri-part split-luciferase system for "add-and-read" detection of anti-TNF therapeutics. In our platform, two small fragments of the split-luciferase, called β9 and β10, are each fused to a different interacting protein. The binding of each of these proteins to anti-TNF antibodies forces the split-luciferase components into proximity where they reform the active luciferase. We identified the fusion proteins, β9-protein A (β9-A) and β10-TNF, as promising binding pairs. We systematically adjusted assay conditions to optimize the signal/background (S/B) ratio, limit of detection (LOD), and percent recovery. The assay has a large dynamic range (0.5-32 μg/mL) and is sensitive enough to monitor both subtherapeutic and supratherapeutic serum concentrations of anti-TNF antibodies, as demonstrated in clinical samples.
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Affiliation(s)
- Sun Jin Kim
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Andrew S. Dixon
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - P. Chad Adamovich
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Parker D. Robinson
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Shawn C. Owen
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Department of Biomedical Engineering, Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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Habazin S, Štambuk J, Šimunović J, Keser T, Razdorov G, Novokmet M. Mass Spectrometry-Based Methods for Immunoglobulin G N-Glycosylation Analysis. Exp Suppl 2021; 112:73-135. [PMID: 34687008 DOI: 10.1007/978-3-030-76912-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mass spectrometry and its hyphenated techniques enabled by the improvements in liquid chromatography, capillary electrophoresis, novel ionization, and fragmentation modes are truly a cornerstone of robust and reliable protein glycosylation analysis. Boost in immunoglobulin G (IgG) glycan and glycopeptide profiling demands for both applied biomedical and research applications has brought many new advances in the field in terms of technical innovations, sample preparation, improved throughput, and confidence in glycan structural characterization. This chapter summarizes mass spectrometry basics, focusing on IgG and monoclonal antibody N-glycosylation analysis on several complexity levels. Different approaches, including antibody enrichment, glycan release, labeling, and glycopeptide preparation and purification, are covered and illustrated with recent breakthroughs and examples from the literature omitting excessive theoretical frameworks. Finally, selected highly popular methodologies in IgG glycoanalytics such as liquid chromatography-mass spectrometry and matrix-assisted laser desorption ionization are discussed more thoroughly yet in simple terms making this text a practical starting point either for the beginner in the field or an experienced clinician trying to make sense out of the IgG glycomic or glycoproteomic dataset.
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Affiliation(s)
- Siniša Habazin
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Jerko Štambuk
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | | | - Toma Keser
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | | | - Mislav Novokmet
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia.
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4
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Paloni M, Cavallotti C. Molecular Modeling of the Interaction of Protein L with Antibodies. ACS Omega 2017; 2:6464-6472. [PMID: 31457247 PMCID: PMC6645367 DOI: 10.1021/acsomega.7b01123] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 09/27/2017] [Indexed: 06/10/2023]
Abstract
Protein L (PpL) is a bacterial protein which is used in the affinity chromatography stage of the production of monoclonal antibodies because of its ability to form high affinity complexes with the light chains of immunoglobulins. In the present work, the binding interfaces between one domain of PpL and antigen-binding fragments (Fab) have been investigated adopting molecular dynamics with the aim of determining the binding contribution of the residues located at the Fab-PpL interface. Because it is known that PpL binds antibodies through two distinct binding sites with different affinities, simulations were performed for both sites to determine interaction free energies to assess the relative binding contribution of the two sites. Mutational studies were then performed only on the dominant binding site. The binding free energy was evaluated with the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) and umbrella sampling/weighted histogram analysis methods. Key residues for the formation of the dominant binding site complex were identified by means of alanine scanning performed both for the Fab and PpL domains. Residues of the light chain of the antibody that contribute most to binding were found to be located between SER7 and VAL13. Four residues from PpL are important for the stability of the complex: PHE839, LYS840, GLU849, and TYR853. Three residues of PpL that do not contribute to the interaction were mutated to histidine (HIS), which changes its protonation state as a function of pH, to find whether this could allow us to control the binding interaction energy. This can be useful in the elution stage of the affinity chromatography purification of antibodies if PpL is used as a ligand. These residues are GLN835, THR836, and ALA837. Molecular dynamics simulations with both protonated and unprotonated HIS were performed to mimic how changing pH may reflect on protein-ligand interaction energies. The MMPBSA approach was used to evaluate the variation of the affinity of the mutated systems with reference to the wild type. Our results show that these mutations could help in disrupting the complex under acidic conditions without impairing the affinity of PpL for the light chains at higher pHs.
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Julian MC, Lee CC, Tiller KE, Rabia LA, Day EK, Schick AJ, Tessier PM. Co-evolution of affinity and stability of grafted amyloid-motif domain antibodies. Protein Eng Des Sel 2015; 28:339-50. [PMID: 26386257 DOI: 10.1093/protein/gzv050] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/17/2015] [Indexed: 11/12/2022] Open
Abstract
An attractive approach for designing lead antibody candidates is to mimic natural protein interactions by grafting peptide recognition motifs into the complementarity-determining regions (CDRs). We are using this approach to generate single-domain (VH) antibodies specific for amyloid-forming proteins such as the Alzheimer's Aβ peptide. Here, we use random mutagenesis and yeast surface display to improve the binding affinity of a lead VH domain grafted with Aβ residues 33-42 in CDR3. Interestingly, co-selection for improved Aβ binding and VH display on the surface of yeast yields antibody domains with improved affinity and reduced stability. The highest affinity VH domains were strongly destabilized on the surface of yeast as well as unfolded when isolated as autonomous domains. In contrast, stable VH domains with improved affinity were reliably identified using yeast surface display by replacing the display antibody that recognizes a linear epitope tag at the terminus of both folded and unfolded VH domains with a conformational ligand (Protein A) that recognizes a discontinuous epitope on the framework of folded VH domains. Importantly, we find that selection for improved stability using Protein A without simultaneous co-selection for improved Aβ binding leads to strong enrichment for stabilizing mutations that reduce antigen binding. Our findings highlight the importance of simultaneously optimizing affinity and stability to improve the rapid isolation of well-folded and specific antibody fragments.
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Affiliation(s)
- Mark C Julian
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Christine C Lee
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Kathryn E Tiller
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Lilia A Rabia
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Evan K Day
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Arthur J Schick
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Peter M Tessier
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Kim DY, To R, Kandalaft H, Ding W, van Faassen H, Luo Y, Schrag JD, St-Amant N, Hefford M, Hirama T, Kelly JF, MacKenzie R, Tanha J. Antibody light chain variable domains and their biophysically improved versions for human immunotherapy. MAbs 2014; 6:219-35. [PMID: 24423624 PMCID: PMC3929445 DOI: 10.4161/mabs.26844] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We set out to gain deeper insight into the potential of antibody light chain variable domains (VLs) as immunotherapeutics. To this end, we generated a naïve human VL phage display library and, by using a method previously shown to select for non-aggregating antibody heavy chain variable domains (VHs), we isolated a diversity of VL domains by panning the library against B cell super-antigen protein L. Eight domains representing different germline origins were shown to be non-aggregating at concentrations as high as 450 µM, indicating VL repertoires are a rich source of non-aggregating domains. In addition, the VLs demonstrated high expression yields in E. coli, protein L binding and high reversibility of thermal unfolding. A side-by-side comparison with a set of non-aggregating human VHs revealed that the VLs had similar overall profiles with respect to melting temperature (Tm), reversibility of thermal unfolding and resistance to gastrointestinal proteases. Successful engineering of a non-canonical disulfide linkage in the core of VLs did not compromise the non-aggregation state or protein L binding properties. Furthermore, the introduced disulfide bond significantly increased their Tms, by 5.5–17.5 °C, and pepsin resistance, although it somewhat reduced expression yields and subtly changed the structure of VLs. Human VLs and engineered versions may make suitable therapeutics due to their desirable biophysical features. The disulfide linkage-engineered VLs may be the preferred therapeutic format because of their higher stability, especially for oral therapy applications that necessitate high resistance to the stomach’s acidic pH and pepsin.
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Affiliation(s)
- Dae Young Kim
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Rebecca To
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Hiba Kandalaft
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Wen Ding
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Henk van Faassen
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Yan Luo
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Joseph D Schrag
- Human Health Therapeutics; National Research Council Canada; Montréal, QC Canada
| | - Nadereh St-Amant
- Centre for Vaccine Evaluation; Biologics and Genetic Therapies Directorate;, Health Canada; Ottawa, ON Canada
| | - Mary Hefford
- Centre for Vaccine Evaluation; Biologics and Genetic Therapies Directorate;, Health Canada; Ottawa, ON Canada
| | - Tomoko Hirama
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - John F Kelly
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Roger MacKenzie
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada; School of Environmental Sciences; Ontario Agricultural College; University of Guelph; Guelph, ON Canada
| | - Jamshid Tanha
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada; School of Environmental Sciences; Ontario Agricultural College; University of Guelph; Guelph, ON Canada; Department of Biochemistry, Microbiology, and Immunology; University of Ottawa; Ottawa, ON Canada
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Hopf TA, Schärfe CPI, Rodrigues JPGLM, Green AG, Kohlbacher O, Sander C, Bonvin AMJJ, Marks DS. Sequence co-evolution gives 3D contacts and structures of protein complexes. eLife 2014; 3. [PMID: 25255213 PMCID: PMC4360534 DOI: 10.7554/elife.03430] [Citation(s) in RCA: 332] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 09/23/2014] [Indexed: 12/24/2022] Open
Abstract
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein-protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein-protein interaction networks and used for interaction predictions at residue resolution.
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Affiliation(s)
- Thomas A Hopf
- Department of Systems Biology, Harvard University, Boston, United States
| | | | - João P G L M Rodrigues
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Anna G Green
- Department of Systems Biology, Harvard University, Boston, United States
| | - Oliver Kohlbacher
- Applied Bioinformatics, Quantitative Biology Center, University of Tübingen, Tübingen, Germany
| | - Chris Sander
- Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Alexandre M J J Bonvin
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Debora S Marks
- Department of Systems Biology, Harvard University, Boston, United States
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Seo JS, Poulter CD. Sandwich antibody arrays using recombinant antibody-binding protein L. Langmuir 2014; 30:6629-6635. [PMID: 24841983 PMCID: PMC4059220 DOI: 10.1021/la500822w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/16/2014] [Indexed: 06/01/2023]
Abstract
Antibody arrays are a useful for detecting antigens and other antibodies. This technique typically requires a uniform and well-defined orientation of antibodies attached to a surface for optimal performance. A uniform orientation can be achieved by modification of antibodies to include a single site for attachment. Thus, uniformly oriented antibody arrays require a bioengineered modification for the antibodies directly immobilization on the solid surface. In this study, we describe a "sandwich-type" antibody array where unmodified antibodies are oriented through binding with regioselectively immobilized recombinant antibody-binding protein L. Recombinant proL-CVIA bearing C-terminal CVIA motif is post-translationally modified with an alkyne group by protein farnesyltransferase (PFTase) at the cysteine residue in the CVIA sequence to give proL-CVIApf, which is covalently attached to an azido-modified glass slide by a Huisgen [3 + 2] cycloaddition reaction. Slides bearing antibodies bound to slides coated with regioselectively immobilized proL-CVIApf gave stronger fluorescence outputs and those where the antibody-binding protein was immobilized in random orientations on an epoxy-modified slide. Properly selected capture and detection antibodies did not cross-react with immobilized proL-CVIApf in sandwich arrays, and the proL-CVIApf slides can be used for multiple cycles of detected over a period of several months.
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Seo JS, Lee S, Poulter CD. Regioselective covalent immobilization of recombinant antibody-binding proteins A, G, and L for construction of antibody arrays. J Am Chem Soc 2013; 135:8973-80. [PMID: 23746333 DOI: 10.1021/ja402447g] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Immobilized antibodies are useful for the detection of antigens in highly sensitive microarray diagnostic applications. Arrays with the antibodies attached regioselectively in a uniform orientation are typically more sensitive than those with random orientations. Direct regioselective immobilization of antibodies on a solid support typically requires a modified form of the protein. We now report a general approach for the regioselective attachment of antibodies to a surface using truncated forms of antibody-binding proteins A, G, and L that retain the structural motifs required for antibody binding. The recombinant proteins have a C-terminal CVIX protein farnesyltransferase recognition motif that allows us to append a bioorthogonal azide or alkyne moiety and use the Cu(I)-catalyzed Huisgen cycloaddition to attach the binding proteins to a suitably modified glass surface. This approach offers several advantages. The recombinant antibody-binding proteins are produced in Escherichia coli, chemoselectively modified posttranslationally in the cell-free homogenate, and directly attached to the glass surface without the need for purification at any stage of the process. Complexes between immobilized recombinant proteins A, G, and L and their respective strongly bound antibodies were stable to repeated washing with PBST buffer at pH 7.2. However, the antibodies could be stripped from the slides by treatment with 0.1 M glycine·HCl buffer, pH 2.6, for 30 min and regenerated by shaking with PBS buffer, pH 7.2, at 4 °C overnight. The recombinant forms of proteins A, G, and L can be used separately or in combination to give glass surfaces capable of binding a wide variety of antibodies.
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Affiliation(s)
- Jin-soo Seo
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
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10
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Abstract
Protein-protein interactions are essential for life. They are responsible for most cellular functions and when they go awry often lead to disease. Proteins are inherently complex. They are flexible macromolecules whose constituent amino acid components act in combinatorial and networked ways when they engage one another in binding interactions. It is just this complexity that allows them to conduct such a broad array of biological functions. Despite decades of intense study of the molecular basis of protein-protein interactions, key gaps in our understanding remain, hindering our ability to accurately predict the specificities and affinities of their interactions. Until recently, most protein-protein investigations have been probed experimentally at the single-amino acid level, making them, by definition, incapable of capturing the combinatorial nature of, and networked communications between, the numerous residues within and outside of the protein-protein interface. This aspect of protein-protein interactions, however, is emerging as a major driving force for protein affinity and specificity. Understanding a combinatorial process necessarily requires a combinatorial experimental tool. Much like the organisms in which they reside, proteins naturally evolve over time, through a combinatorial process of mutagenesis and selection, to functionally associate. Elucidating the process by which proteins have evolved may be one of the keys to deciphering the molecular rules that govern their interactions with one another. Directed evolution is a technique performed in the laboratory that mimics natural evolution on a tractable time scale that has been utilized widely to engineer proteins with novel capabilities, including altered binding properties. In this review, we discuss directed evolution as an emerging tool for dissecting protein-protein interactions.
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Affiliation(s)
- Daniel A Bonsor
- Boston Biomedical Research Institute, 64 Grove Street, Watertown, Massachusetts 02472, United States
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MacKenzie DA, Tailford LE, Hemmings AM, Juge N. Crystal structure of a mucus-binding protein repeat reveals an unexpected functional immunoglobulin binding activity. J Biol Chem 2009; 284:32444-53. [PMID: 19758995 DOI: 10.1074/jbc.m109.040907] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Lactobacillus reuteri mucus-binding protein (MUB) is a cell-surface protein that is involved in bacterial interaction with mucus and colonization of the digestive tract. The 353-kDa mature protein is representative of a broadly important class of adhesins that have remained relatively poorly characterized due to their large size and highly modular nature. MUB contains two different types of repeats (Mub1 and Mub2) present in six and eight copies, respectively, and shown to be responsible for the adherence to intestinal mucus. Here we report the 1.8-A resolution crystal structure of a type 2 Mub repeat (184 amino acids) comprising two structurally related domains resembling the functional repeat found in a family of immunoglobulin (Ig)-binding proteins. The N-terminal domain bears striking structural similarity to the repeat unit of Protein L (PpL) from Peptostreptococcus magnus, suggesting binding in a non-immune Fab-dependent manner. A distorted PpL-like fold is also seen in the C-terminal domain. As with PpL, Mub repeats were able to interact in vitro with a large repertoire of mammalian Igs, including secretory IgA. This hitherto undetected activity is consistent with the current model that antibody responses against commensal flora are of broad specificity and low affinity.
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Affiliation(s)
- Donald A MacKenzie
- Institute of Food Research, Colney Lane, Norwich NR4 7UA, United Kingdom
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12
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Abstract
The interaction of insulin with its receptor is complex. Kinetic and equilibrium binding studies suggest coexistence of high- and low-affinity binding sites or negative cooperativity. These phenomena and high-affinity interactions are dependent on the dimeric structure of the receptor. Structure-function studies of insulin analogs suggest insulin has two receptor binding sites, implying a bivalent interaction with the receptor. Alanine scanning studies of the secreted recombinant receptor implicate the L1 domain and a C-terminal peptide of the receptor alpha subunit as components of one ligand binding site. Functional studies suggest that the first and second type III fibronectin repeats of the receptor contain a second ligand binding site. We have used structure-directed alanine scanning mutagenesis to identify determinants in these domains involved in ligand interactions. cDNAs encoding alanine mutants of the holo-receptor were transiently expressed in 293 cells, and the binding properties of the expressed receptor were determined. Alanine mutations of Lys(484), Leu(552), Asp(591), Ile(602), Lys(616), Asp(620), and Pro(621) compromised affinities for insulin 2-5-fold. With the exception of Asp(620), none of these mutations compromised the affinity of the recombinant secreted receptor for insulin, indicating that the perturbation of the interaction is at the site of mutation and not an indirect effect on the interaction with the binding site of the secreted receptor. These residues thus form part of a novel ligand binding site of the insulin receptor. Complementation experiments demonstrate that insulin interacts in trans with both receptor binding sites to generate high-affinity interactions.
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Affiliation(s)
- Linda Whittaker
- Department of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Dell'Orco D. Fast predictions of thermodynamics and kinetics of protein-protein recognition from structures: from molecular design to systems biology. Mol Biosyst 2009; 5:323-34. [PMID: 19396368 DOI: 10.1039/b821580d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The increasing call for an overall picture of the interactions between the components of a biological system that give rise to the observed function is often summarized by the expression systems biology. Both the interpretative and predictive capabilities of holistic models of biochemical systems, however, depend to a large extent on the level of physico-chemical knowledge of the individual molecular interactions making up the network. This review is focused on the structure-based quantitative characterization of protein-protein interactions, ubiquitous in any biochemical pathway. Recently developed, fast and effective computational methods are reviewed, which allow the assessment of kinetic and thermodynamic features of the association-dissociation processes of protein complexes, both in water soluble and membrane environments. The performance and the accuracy of fast and semi-empirical structure-based methods have reached comparable levels with respect to the classical and more elegant molecular simulations. Nevertheless, the broad accessibility and lower computational cost provide the former methods with the advantageous possibility to perform systems-level analyses including extensive in silico mutagenesis screenings and large-scale structural predictions of multiprotein complexes.
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Affiliation(s)
- Daniele Dell'Orco
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41100, Modena, Italy.
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14
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Reichmann D, Rahat O, Cohen M, Neuvirth H, Schreiber G. The molecular architecture of protein-protein binding sites. Curr Opin Struct Biol 2007; 17:67-76. [PMID: 17239579 DOI: 10.1016/j.sbi.2007.01.004] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 12/13/2006] [Accepted: 01/10/2007] [Indexed: 11/16/2022]
Abstract
The formation of specific protein interactions plays a crucial role in most, if not all, biological processes, including signal transduction, cell regulation, the immune response and others. Recent advances in our understanding of the molecular architecture of protein-protein binding sites, which facilitates such diversity in binding affinity and specificity, are enabling us to address key questions. What is the amino acid composition of binding sites? What are interface hotspots? How are binding sites organized? What are the differences between tight and weak interacting complexes? How does water contribute to binding? Can the knowledge gained be translated into protein design? And does a universal code for binding exist, or is it the architecture and chemistry of the interface that enable diverse but specific binding solutions?
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Affiliation(s)
- Dana Reichmann
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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15
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Abstract
This work investigated the adsorption of autoantibodies such as anti-SS-A/Ro, anti-SS-B/La, anti-Sm, and anti-dsDNA on protein L-agarose gel. In order to determine better conditions for IgG adsorption on this matrix, some buffer systems were tested. Adsorption data were analyzed using the Langmuir and Langmuir-Freundlich isotherm models. The experimental isotherms were best described by the Langmuir-Freundlich model, which indicated negative and positive cooperativities for binding in the presence of PBS and HEPES buffers, respectively. The K(d) values for phosphate buffered saline solution (PBS) and hydroxyethylpiperazine ethanesulfonic acid (HEPES) were 2.8 x 10(-7) M and 3.2 x 10(-7) M, respectively, which indicate a high affinity between IgG and the immobilized protein L. The amount of protein adsorbed per amount of protein loaded was high for anti-Sm (44%) and anti-dsDNA (46%), but low for anti-SS-B/La (9%). The amount of albumin adsorbed was lower than 0.06 mg/mL, which may remove the need for a plasma replacement solution in clinical apheresis.
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Affiliation(s)
- Isa Santos Duarte
- Departamento de Processos Biotecnológicos, Faculdade de Engenharia Química, Universidade Estadual de Campinas, Campinas, SP, Brazil
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Khursigara CM, De Crescenzo G, Pawelek PD, Coulton JW. Deletion of the proline-rich region of TonB disrupts formation of a 2:1 complex with FhuA, an outer membrane receptor of Escherichia coli. Protein Sci 2005; 14:1266-73. [PMID: 15802653 PMCID: PMC2253273 DOI: 10.1110/ps.051342505] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
TonB protein of Escherichia coli couples the electrochemical potential of the cytoplasmic membrane (CM) to active transport of iron-siderophores and vitamin B(12) across the outer membrane (OM). TonB interacts with OM receptors and transduces conformationally stored energy. Energy for transport is provided by the proton motive force through ExbB and ExbD, which form a ternary complex with TonB in the CM. TonB contains three distinct domains: an N-terminal signal/anchor sequence, a C-terminal domain, and a proline-rich region. The proline-rich region was proposed to extend TonB's structure across the periplasm, allowing it to contact spatially distant OM receptors. Having previously identified a 2:1 stoichiometry for the complex of full-length (FL) TonB and the OM receptor FhuA, we now demonstrate that deletion of the proline-rich region of TonB (TonBDelta66-100) prevents formation of the 2:1 complex. Sedimentation velocity analytical ultracentrifugation of TonBDelta66-100 with FhuA revealed that a 1:1 TonB-FhuA complex is formed. Interactions between TonBDelta66-100 and FhuA were assessed by surface plasmon resonance, and their affinities were determined to be similar to those of TonB (FL)-FhuA. Presence of the FhuA-specific siderophore ferricrocin altered neither stoichiometry nor affinity of interaction, leading to our conclusion that the proline-rich region in TonB is important in forming a 2:1 high-affinity TonB-FhuA complex in vitro. Furthermore, TonBDelta66-100-FhuADelta21-128 interactions demonstrated that the cork region of the OM receptor was also important in forming a complex. Together, these results demonstrate a novel function of the proline-rich region of TonB in mediating TonB-TonB interactions within the TonB-FhuA complex.
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Affiliation(s)
- Cezar M Khursigara
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Quebec, Canada H3A 2B4
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Enever C, Tomlinson IM, Lund J, Levens M, Holliger P. Engineering High Affinity Superantigens by Phage Display. J Mol Biol 2005; 347:107-20. [PMID: 15733921 DOI: 10.1016/j.jmb.2005.01.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Revised: 12/10/2004] [Accepted: 01/05/2005] [Indexed: 11/22/2022]
Abstract
Protein L (PpL) is a B-cell superantigen from Peptostreptococcus magnus known to bind to mammalian Vkappa light chains. PpL from P.magnus strain 312 comprises five homologous immunoglobulin (Ig) binding domains. We first analysed the binding of the individual domains (B1-B5) of PpL(312) to human Vkappa light chains (huVkappa) subtypes 1 (huVkappaI) and 3 (huVkappaIII). Using a combination of rational design and phage selection we isolated mutants of the N-terminal B1 domain with a 14-fold increased affinity for huVkappa1 (B1kappa1) and >tenfold increased affinity for huVkappaIII (B1kappa3). We investigated the potential of the selected domains, in particular the B1kappa1 domain, as reagents in immunochemistry and immunotherapy. B1kappa1 proved a superior reagent than the wild-type domain, allowing up to tenfold more sensitive detection of human Vkappa antibody fragments in ELISA. A fusion protein of B1kappa1 with a human Vlambda antibody scFv fragment promoted the efficient recruitment of antibody encoded effector functions including complement, mononuclear phagocyte respiratory burst and phagocytosis through retargeting of IgGkappa and IgMkappa. Our results suggest that superantigens with improved affinity and/or specificity are easily accessible through protein engineering. Such engineered superantigens should prove useful as reagents in immunochemistry and may have potential as agents in immunotherapy.
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Affiliation(s)
- Carolyn Enever
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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Abstract
The year 2004 represents a milestone for the biosensor research community: in this year, over 1000 articles were published describing experiments performed using commercially available systems. The 1038 papers we found represent an approximately 10% increase over the past year and demonstrate that the implementation of biosensors continues to expand at a healthy pace. We evaluated the data presented in each paper and compiled a 'top 10' list. These 10 articles, which we recommend every biosensor user reads, describe well-performed kinetic, equilibrium and qualitative/screening studies, provide comparisons between binding parameters obtained from different biosensor users, as well as from biosensor- and solution-based interaction analyses, and summarize the cutting-edge applications of the technology. We also re-iterate some of the experimental pitfalls that lead to sub-optimal data and over-interpreted results. We are hopeful that the biosensor community, by applying the hints we outline, will obtain data on a par with that presented in the 10 spotlighted articles. This will ensure that the scientific community at large can be confident in the data we report from optical biosensors.
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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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