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1.
J Mol Biol ; 434(12): 167602, 2022 06 30.
Article in English | MEDLINE | ID: mdl-35469831

ABSTRACT

High performance affinity reagents are essential tools to enable biologists to profile the cellular location and composition of macromolecular complexes undergoing dynamic reorganization. To support further development of such tools, we have assembled a high-throughput phage display pipeline to generate Fab-based affinity reagents that target different dynamic forms of a large macromolecular complex, using the Chromosomal Passenger Complex (CPC), as an example. The CPC is critical for the maintenance of chromosomal and cytoskeleton processes during cell division. The complex contains 4 protein components: Aurora B kinase, survivin, borealin and INCENP. The CPC acts as a node to dynamically organize other partnering subcomplexes to build multiple functional structures during mitotic progression. Using phage display mutagenesis, a cohort of synthetic antibodies (sABs) were generated against different domains of survivin, borealin and INCENP. Immunofluorescence established that a set of these sABs can discriminate between the form of the CPC complex in the midbody versus the spindle. Others localize to targets, which appear to be less organized, in the nucleus or cytoplasm. This differentiation suggests that different CPC epitopes have dynamic accessibility depending upon the mitotic state of the cell. An Immunoprecipitation/Mass Spectrometry analysis was performed using sABs that bound specifically to the CPC in either the midbody or MT spindle macromolecular assemblies. Thus, sABs can be exploited as high performance reagents to profile the accessibility of different components of the CPC within macromolecular assemblies during different stages of mitosis suggesting this high throughput approach will be applicable to other complex macromolecular systems.


Subject(s)
Antibodies , Aurora Kinase B , Cell Cycle Proteins , Chromosomal Proteins, Non-Histone , Immunoglobulin Fab Fragments , Multiprotein Complexes , Survivin , Antibodies/chemistry , Antibodies/genetics , Aurora Kinase B/analysis , Aurora Kinase B/immunology , Cell Cycle Proteins/analysis , Cell Cycle Proteins/immunology , Chromosomal Proteins, Non-Histone/analysis , Chromosomal Proteins, Non-Histone/immunology , Cytoskeleton/metabolism , Humans , Immunoglobulin Fab Fragments/chemistry , Immunoglobulin Fab Fragments/genetics , Mitosis , Multiprotein Complexes/analysis , Multiprotein Complexes/immunology , Peptide Library , Phosphorylation , Spindle Apparatus/metabolism , Survivin/chemistry , Survivin/metabolism
2.
Cell ; 183(2): 429-441.e16, 2020 10 15.
Article in English | MEDLINE | ID: mdl-32941803

ABSTRACT

Novel COVID-19 therapeutics are urgently needed. We generated a phage-displayed human antibody VH domain library from which we identified a high-affinity VH binder ab8. Bivalent VH, VH-Fc ab8, bound with high avidity to membrane-associated S glycoprotein and to mutants found in patients. It potently neutralized mouse-adapted SARS-CoV-2 in wild-type mice at a dose as low as 2 mg/kg and exhibited high prophylactic and therapeutic efficacy in a hamster model of SARS-CoV-2 infection, possibly enhanced by its relatively small size. Electron microscopy combined with scanning mutagenesis identified ab8 interactions with all three S protomers and showed how ab8 neutralized the virus by directly interfering with ACE2 binding. VH-Fc ab8 did not aggregate and did not bind to 5,300 human membrane-associated proteins. The potent neutralization activity of VH-Fc ab8 combined with good developability properties and cross-reactivity to SARS-CoV-2 mutants provide a strong rationale for its evaluation as a COVID-19 therapeutic.


Subject(s)
Coronavirus Infections/drug therapy , Immunoglobulin Heavy Chains/administration & dosage , Immunoglobulin Variable Region/administration & dosage , Peptide Library , Pneumonia, Viral/drug therapy , Angiotensin-Converting Enzyme 2 , Animals , Antibodies, Neutralizing/immunology , Antibodies, Neutralizing/ultrastructure , Antibodies, Viral/administration & dosage , Antibodies, Viral/chemistry , Antibodies, Viral/immunology , Antibodies, Viral/ultrastructure , Antibody Affinity , COVID-19 , Cricetinae , Female , Humans , Immunoglobulin Fc Fragments/immunology , Immunoglobulin Heavy Chains/chemistry , Immunoglobulin Heavy Chains/immunology , Immunoglobulin Heavy Chains/ultrastructure , Immunoglobulin Variable Region/chemistry , Immunoglobulin Variable Region/immunology , Immunoglobulin Variable Region/ultrastructure , Mice , Mice, Inbred BALB C , Mutation , Pandemics , Peptidyl-Dipeptidase A/metabolism , Protein Domains , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism , Spike Glycoprotein, Coronavirus/ultrastructure , COVID-19 Drug Treatment
3.
J Mol Biol ; 427(16): 2707-25, 2015 Aug 14.
Article in English | MEDLINE | ID: mdl-26159704

ABSTRACT

Reversible, high-affinity immobilization tags are critical tools for myriad biological applications. However, inherent issues are associated with a number of the current methods of immobilization. Particularly, a critical element in phage display sorting is functional immobilization of target proteins. To circumvent these problems, we have used a mutant (N5A) of calmodulin binding peptide (CBP) as an immobilization tag in phage display sorting. The immobilization relies on the ultra high affinity of calmodulin to N5A mutant CBP (RWKKNFIAVSAANRFKKIS) in presence of calcium (KD~2 pM), which can be reversed by EDTA allowing controlled "capture and release" of the specific binders. To evaluate the capabilities of this system, we chose eight targets, some of which were difficult to overexpress and purify with other tags and some had failed in sorting experiments. In all cases, specific binders were generated using a Fab phage display library with CBP-fused constructs. KD values of the Fabs were in subnanomolar to low nanomolar (nM) ranges and were successfully used to selectively recognize antigens in cell-based experiments. Some of these targets were problematic even without any tag; thus, the fact that all led to successful selection endpoints means that borderline cases can be worked on with a high probability of a positive outcome. Taken together with examples of successful case specific, high-level applications like generation of conformation-, epitope- and domain-specific Fabs, we feel that the CBP tag embodies all the attributes of covalent immobilization tags but does not suffer from some of their well-documented drawbacks.


Subject(s)
Calmodulin-Binding Proteins/chemistry , Calmodulin-Binding Proteins/genetics , Calmodulin/metabolism , Cell Surface Display Techniques/methods , Adaptor Proteins, Signal Transducing/genetics , Amino Acid Sequence , Animals , Biotinylation , Cell Line , HEK293 Cells , Histone-Lysine N-Methyltransferase , Humans , Maltose-Binding Proteins/chemistry , Maltose-Binding Proteins/genetics , Mice , Protein Binding/genetics , Protein Methyltransferases/genetics , ras GTPase-Activating Proteins/genetics
4.
J Immunol Methods ; 415: 24-30, 2014 Dec 15.
Article in English | MEDLINE | ID: mdl-25450256

ABSTRACT

Immunoglobulin binding proteins (IBPs) are broadly used as reagents for the purification and detection of antibodies. Among the IBPs, the most widely used are Protein-A and Protein-G. The C2 domain of Protein-G from Streptococcus is a multi-specific protein domain; it possesses a high affinity (K(D) ~10 nM) for the Fc region of the IgG, but a much lower affinity (KD~low µM) for the constant domain of the antibody fragment (Fab), which limits some of its applications. Here, we describe the engineering of the Protein-G interface using phage display to create Protein-G-A1, a variant with 8 point mutations and an approximately 100-fold improved affinity over the parent domain for the 4D5 Fab scaffold. Protein-G-A1 is capable of robust binding to Fab fragments for numerous applications. Furthermore, we isolated a variant with pH-dependent affinity, demonstrating a 1,000-fold change in affinity from pH7 to 4. Additional rational mutagenesis endowed Protein-G with significantly enhanced stability in basic conditions relative to the parent domain while maintaining high affinity to the Fab. This property is particularly useful to regenerate Protein-G affinity columns. Lastly, the affinity-matured Protein-G-A1 variant was tethered together to produce dimers capable of providing multivalent affinity enhancement to a low affinity antibody fragment-antigen interaction. Engineered Protein-G variants should find widespread application in the use of Fab-based affinity reagents.


Subject(s)
Bacterial Proteins/chemistry , Immunoglobulin Fab Fragments/chemistry , Immunoglobulin Fc Fragments/chemistry , Immunoglobulin G/chemistry , Amino Acid Sequence , Antibody Affinity , Bacterial Proteins/genetics , Bacterial Proteins/immunology , Hydrogen-Ion Concentration , Immunoglobulin Fab Fragments/genetics , Immunoglobulin Fab Fragments/immunology , Immunoglobulin Fc Fragments/genetics , Immunoglobulin Fc Fragments/immunology , Immunoglobulin G/genetics , Immunoglobulin G/immunology , Kinetics , Molecular Sequence Data , Mutation , Peptide Library , Protein Binding , Protein Engineering/methods , Protein Structure, Tertiary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/immunology
5.
Med Sci Monit ; 15(7): BR194-201, 2009 Jul.
Article in English | MEDLINE | ID: mdl-19564819

ABSTRACT

BACKGROUND: Chronic inflammation and remodeling of the bronchial wall are basic hallmarks of asthma. It is known that mesenchymal cells in the lamina reticularis underlying the basement membrane of the thickened airway wall of asthmatics predominantly display the phenotype of myofibroblasts and express alpha-smooth muscle actin (alpha-SMA). Human bronchial fibroblasts (HBFs) transform in vitro into myofibroblasts under the influence of transforming growth factor (TGF-beta). Differences in the reactivity of fibroblasts to TGF-beta in cultures derived from healthy and asthmatic donors are elucidated here. MATERIAL/METHODS: Primary human bronchial fibroblasts (HBFs) were cultured from bronchial biopsies from non-asthmatic (n=7) and asthmatic (n=7) donors and treated with TGF-beta1 or TGF-beta2 to induce myofibroblast differentiation. Expression of alpha-smooth muscle actin (alpha-SMA) was assessed by immunocytochemistry and Western blotting. The cell size and shape parameters were measured by computer-aided methods. RESULTS: Regardless of whether TGF-beta1 or TGF-beta2 was used, asthmatic cells showed enhanced expression of the myofibroblast marker as confirmed by immunocytochemistry and immunoblotting. Analysis of the shape parameters of cells incubated in the presence of TGF-beta1 revealed that HBFs of asthmatics differ from those of non-asthmatics. CONCLUSIONS: It is concluded that asthmatic HBFs cultured in vitro display some inherent features which facilitate their differentiation into myofibroblasts. These data indicate that increased reactivity of asthmatic fibroblasts to TGF-beta may play a crucial role in asthma.


Subject(s)
Asthma/pathology , Cell Differentiation , Fibroblasts/cytology , Actins/metabolism , Cell Differentiation/drug effects , Cell Shape/drug effects , Cell Size/drug effects , Cells, Cultured , Female , Fibroblasts/drug effects , Humans , Male , Middle Aged , Transforming Growth Factor beta1/pharmacology
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