1
|
Neira JL, Rizzuti B, Abian O, Velazquez-Campoy A. Isolated auto-citrullinated regions of PADI4 associate to the intact protein without altering their disordered conformation. Biophys Chem 2024; 312:107288. [PMID: 38991454 DOI: 10.1016/j.bpc.2024.107288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 06/19/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024]
Abstract
PADI4 is one of the human isoforms of a group of enzymes intervening in the conversion of arginine to citrulline. It is involved in the development of several types of tumors, as well as other immunological illnesses, such as psoriasis, multiple sclerosis, or rheumatoid arthritis. PADI4 auto-citrullinates in several regions of its sequence, namely in correspondence of residues Arg205, Arg212, Arg218, and Arg383. We wanted to study whether the citrullinated moiety affects the conformation of nearby regions and its binding to intact PADI4. We designed two series of synthetic peptides comprising either the wild-type or the relative citrullinated versions of such regions - i.e., a first series of peptides comprising the first three arginines, and a second series comprising Arg383. We studied their conformational properties in isolation by using fluorescence, far-ultraviolet (UV) circular dichroism (CD), and 2D1H NMR. Furthermore, we characterized the binding of the wild-type and citrullinated peptides in the two series to the intact PADI4, by using isothermal titration calorimetry (ITC), fluorescence, and biolayer interferometry (BLI), as well as by molecular docking simulations. We observed that citrullination did not alter the local conformational propensities of the isolated peptides. Nevertheless, for all the peptides in the two series, citrullination slowed down the kinetic koff rates of the binding reaction to PADI4, probably due to differences in electrostatic effects compared to the presence of arginine. The affinities of PADI4 for unmodified peptides were slightly larger than those of the corresponding citrullinated ones in the two series, but they were all within the same range, indicating that there were no relevant variations in the thermodynamics of binding due to sequence effects. These results highlight details of the self-citrullination of PADI4 and, more generally, of possible auto-catalytic mechanisms taking place in vivo for other citrullinating enzymes or, alternatively, in proteins undergoing citrullination passively.
Collapse
Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Bruno Rizzuti
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Olga Abian
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| |
Collapse
|
2
|
Leimu L, Holm P, Gąciarz A, Haavisto O, Prince S, Pesonen U, Huovinen T, Lamminmäki U. Epitope-specific antibody fragments block aggregation of AGelD187N, an aberrant peptide in gelsolin amyloidosis. J Biol Chem 2024; 300:107507. [PMID: 38944121 PMCID: PMC11298591 DOI: 10.1016/j.jbc.2024.107507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
Aggregation of aberrant fragment of plasma gelsolin, AGelD187N, is a crucial event underlying the pathophysiology of Finnish gelsolin amyloidosis, an inherited form of systemic amyloidosis. The amyloidogenic gelsolin fragment AGelD187N does not play any physiological role in the body, unlike most aggregating proteins related to other protein misfolding diseases. However, no therapeutic agents that specifically and effectively target and neutralize AGelD187N exist. We used phage display technology to identify novel single-chain variable fragments that bind to different epitopes in the monomeric AGelD187N that were further maturated by variable domain shuffling and converted to antigen-binding fragment (Fab) antibodies. The generated antibody fragments had nanomolar binding affinity for full-length AGelD187N, as evaluated by biolayer interferometry. Importantly, all four Fabs selected for functional studies efficiently inhibited the amyloid formation of full-length AGelD187N as examined by thioflavin fluorescence assay and transmission electron microscopy. Two Fabs, neither of which bound to the previously proposed fibril-forming region of AGelD187N, completely blocked the amyloid formation of AGelD187N. Moreover, no small soluble aggregates, which are considered pathogenic species in protein misfolding diseases, were formed after successful inhibition of amyloid formation by the most promising aggregation inhibitor, as investigated by size-exclusion chromatography combined with multiangle light scattering. We conclude that all regions of the full-length AGelD187N are important in modulating its assembly into fibrils and that the discovered epitope-specific anti-AGelD187N antibody fragments provide a promising starting point for a disease-modifying therapy for gelsolin amyloidosis, which is currently lacking.
Collapse
Affiliation(s)
- Laura Leimu
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland.
| | - Patrik Holm
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; Department of Life Technologies, University of Turku, Turku, Finland; Organon R&D Finland, Turku, Finland
| | - Anna Gąciarz
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; Mobidiag, A Hologic Company, Espoo, Finland
| | - Oskar Haavisto
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Stuart Prince
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; MediCity Research Laboratory, University of Turku, Turku, Finland
| | - Ullamari Pesonen
- Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Tuomas Huovinen
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland.
| |
Collapse
|
3
|
Keeler SP, Wu K, Zhang Y, Mao D, Li M, Iberg CA, Austin SR, Glaser SA, Yantis J, Podgorny S, Brody SL, Chartock JR, Han Z, Byers DE, Romero AG, Holtzman MJ. A potent MAPK13-14 inhibitor prevents airway inflammation and mucus production. Am J Physiol Lung Cell Mol Physiol 2023; 325:L726-L740. [PMID: 37847710 PMCID: PMC11068410 DOI: 10.1152/ajplung.00183.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023] Open
Abstract
Common respiratory diseases continue to represent a major public health problem, and much of the morbidity and mortality is due to airway inflammation and mucus production. Previous studies indicated a role for mitogen-activated protein kinase 14 (MAPK14) in this type of disease, but clinical trials are unsuccessful to date. Our previous work identified a related but distinct kinase known as MAPK13 that is activated in respiratory airway diseases and is required for mucus production in human cell-culture models. Support for MAPK13 function in these models came from effectiveness of MAPK13 versus MAPK14 gene-knockdown and from first-generation MAPK13-14 inhibitors. However, these first-generation inhibitors were incompletely optimized for blocking activity and were untested in vivo. Here we report the next generation and selection of a potent MAPK13-14 inhibitor (designated NuP-3) that more effectively downregulates type-2 cytokine-stimulated mucus production in air-liquid interface and organoid cultures of human airway epithelial cells. We also show that NuP-3 treatment prevents respiratory airway inflammation and mucus production in new minipig models of airway disease triggered by type-2 cytokine challenge or respiratory viral infection. The results thereby provide the next advance in developing a small-molecule kinase inhibitor to address key features of respiratory disease.NEW & NOTEWORTHY This study describes the discovery of a potent mitogen-activated protein kinase 13-14 (MAPK13-14) inhibitor and its effectiveness in models of respiratory airway disease. The findings thereby provide a scheme for pathogenesis and therapy of lung diseases [e.g., asthma, chronic obstructive pulmonary disease (COPD), Covid-19, postviral, and allergic respiratory disease] and related conditions that implicate MAPK13-14 function. The findings also refine a hypothesis for epithelial and immune cell functions in respiratory disease that features MAPK13 as a possible component of this disease process.
Collapse
Affiliation(s)
- Shamus P Keeler
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Kangyun Wu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Yong Zhang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Dailing Mao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Ming Li
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Courtney A Iberg
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | | | - Samuel A Glaser
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Jennifer Yantis
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Stephanie Podgorny
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Steven L Brody
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Joshua R Chartock
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Zhenfu Han
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Derek E Byers
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Arthur G Romero
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Michael J Holtzman
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, United States
- NuPeak Therapeutics Inc., St. Louis, Missouri, United States
| |
Collapse
|
4
|
Neira JL, Palomino-Schätzlein M. Folding of the nascent polypeptide chain of a histidine phosphocarrier protein in vitro. Arch Biochem Biophys 2023; 736:109538. [PMID: 36738980 DOI: 10.1016/j.abb.2023.109538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
The phosphotransferase system (PTS), a metabolic pathway formed by five proteins, modulates the use of sugars in bacteria. The second protein in the chain is the histidine phosphocarrier, HPr, with the binding site at His15. The HPr kinase/phosphorylase (HPrK/P), involved in the bacterial use of carbon sources, phosphorylates HPr at Ser46, and it binds at its binding site. The regulator of sigma D protein (Rsd) also binds to HPr at His15. We have designed fragments of HPr, growing from its N-terminus and containing the His15. In this work, we obtained three fragments, HPr38, HPr58 and HPr70, comprising the first thirty-eight, fifty-eight and seventy residues of HPr, respectively. All fragments were mainly disordered, with evidence of a weak native-like, helical population around the binding site, as shown by fluorescence, far-ultraviolet circular dichroism, size exclusion chromatography and nuclear magnetic resonance. Although HPr38, HPr58 and HPr70 were disordered, they could bind to: (i) the N-terminal domain of first protein of the PTS, EIN; (ii) Rsd; and, (iii) HPrK/P, as shown by fluorescence and biolayer interferometry (BLI). The association constants for each protein to any of the fragments were in the low micromolar range, within the same range than those measured in the binding of HPr to each protein. Then, although acquisition of stable, native-like secondary and tertiary structures occurred at the last residues of the polypeptide, the ability to bind protein partners happened much earlier in the growing chain. Binding was related to the presence of the native-like structure around His15.
Collapse
Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018, Zaragoza, Spain.
| | - Martina Palomino-Schätzlein
- ProtoQSAR SL, CEEI-Valencia, Parque Tecnológico de Valencia, Av. Benjamin Franklin 12 (Dep. 8), 46980, Paterna, Valencia, Spain
| |
Collapse
|
5
|
Rizzuti B, Iovanna JL, Neira JL. Deciphering the Binding of the Nuclear Localization Sequence of Myc Protein to the Nuclear Carrier Importin α3. Int J Mol Sci 2022; 23:ijms232315333. [PMID: 36499669 PMCID: PMC9739371 DOI: 10.3390/ijms232315333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The oncoprotein Myc is a transcription factor regulating global gene expression and modulating cell proliferation, apoptosis, and metabolism. Myc has a nuclear localization sequence (NLS) comprising residues Pro320 to Asp328, to allow for nuclear translocation. We designed a peptide comprising such region and the flanking residues (Ala310-Asn339), NLS-Myc, to study, in vitro and in silico, the ability to bind importin α3 (Impα3) and its truncated species (ΔImpα3) depleted of the importin binding domain (IBB), by using fluorescence, circular dichroism (CD), biolayer interferometry (BLI), nuclear magnetic resonance (NMR), and molecular simulations. NLS-Myc interacted with both importin species, with affinity constants of ~0.5 µM (for Impα3) and ~60 nM (for ΔImpα3), as measured by BLI. The molecular simulations predicted that the anchoring of NLS-Myc took place in the major binding site of Impα3 for the NLS of cargo proteins. Besides clarifying the conformational behavior of the isolated NLS of Myc in solution, our results identified some unique properties in the binding of this localization sequence to the nuclear carrier Impα3, such as a difference in the kinetics of its release mechanism depending on the presence or absence of the IBB domain.
Collapse
Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
- Instituto de Biocomputación y Física de Sistemas Complejos–Unidad Mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Correspondence: (B.R.); (J.L.N.)
| | - Juan L. Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille Université, 13288 Marseille, France
| | - José L. Neira
- Instituto de Biocomputación y Física de Sistemas Complejos–Unidad Mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDIBE), Universidad Miguel Hernández, 03202 Elche, Spain
- Correspondence: (B.R.); (J.L.N.)
| |
Collapse
|
6
|
Human Enzyme PADI4 Binds to the Nuclear Carrier Importin α3. Cells 2022; 11:cells11142166. [PMID: 35883608 PMCID: PMC9319256 DOI: 10.3390/cells11142166] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/13/2022] [Accepted: 07/08/2022] [Indexed: 12/18/2022] Open
Abstract
PADI4 is a peptidyl-arginine deiminase (PADI) involved in the conversion of arginine to citrulline. PADI4 is present in macrophages, monocytes, granulocytes, and several cancer cells. It is the only PADI family member observed within both the nucleus and the cytoplasm. PADI4 has a predicted nuclear localization sequence (NLS) comprising residues Pro56 to Ser83, to allow for nuclear translocation. Recent predictors also suggest that the region Arg495 to Ile526 is a possible NLS. To understand how PADI4 is involved in cancer, we studied the ability of intact PADI4 to bind importin α3 (Impα3), a nuclear transport factor that plays tumor-promoting roles in several cancers, and its truncated species (ΔImpα3) without the importin-binding domain (IBB), by using fluorescence, circular dichroism (CD), and isothermal titration calorimetry (ITC). Furthermore, the binding of two peptides, encompassing the first and the second NLS regions, was also studied using the same methods and molecular docking simulations. PADI4 interacted with both importin species, with affinity constants of ~1–5 µM. The isolated peptides also interacted with both importins. The molecular simulations predict that the anchoring of both peptides takes place in the major binding site of Impα3 for the NLS of cargo proteins. These findings suggest that both NLS regions were essentially responsible for the binding of PADI4 to the two importin species. Our data are discussed within the framework of a cell mechanism of nuclear transport that is crucial in cancer.
Collapse
|
7
|
Applications of Surface Plasmon Resonance and Biolayer Interferometry for Virus–Ligand Binding. Viruses 2022; 14:v14040717. [PMID: 35458446 PMCID: PMC9027846 DOI: 10.3390/v14040717] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/20/2022] [Accepted: 03/26/2022] [Indexed: 02/01/2023] Open
Abstract
Surface plasmon resonance and biolayer interferometry are two common real-time and label-free assays that quantify binding events by providing kinetic parameters. There is increased interest in using these techniques to characterize whole virus-ligand interactions, as the methods allow for more accurate characterization than that of a viral subunit-ligand interaction. This review aims to summarize and evaluate the uses of these technologies specifically in virus–ligand and virus-like particle–ligand binding cases to guide the field towards studies that apply these robust methods for whole virus-based studies.
Collapse
|
8
|
Kuznetsov A, Arukuusk P, Härk H, Juronen E, Ustav M, Langel Ü, Järv J. ACE2 Peptide Fragment Interaction with Different S1 Protein Sites. Int J Pept Res Ther 2021; 28:7. [PMID: 34867130 PMCID: PMC8634746 DOI: 10.1007/s10989-021-10324-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2021] [Indexed: 11/25/2022]
Abstract
We study the effect of the peptide QAKTFLDKFNHEAEDLFYQ on the kinetics of the SARS-CoV-2 spike protein S1 binding to angiotensin-converting enzyme 2 (ACE2), with the aim to characterize the interaction mechanism of the SARS-CoV2 virus with its host cell. This peptide corresponds to the sequence 24–42 of the ACE2 α1 domain, which marks the binding site for the S1 protein. The kinetics of S1-ACE2 complex formation was measured in the presence of various concentrations of the peptide using bio-layer interferometry. Formation of the S1-ACE2 complex was inhibited by the peptide in cases where it was preincubated with S1 protein before the binding experiment. The kinetic analysis of S1-ACE2 complex dissociation revealed that preincubation stabilized this complex, and this effect was dependent on the peptide concentration as well as the preincubation time. The results point to the formation of the ternary complex of S1 with ACE2 and the peptide. This is possible in the presence of another binding site for the S1 protein beside the receptor-binding domain for ACE2, which binds the peptide QAKTFLDKFNHEAEDLFYQ. Therefore, we conducted computational mapping of the S1 protein surface, revealing two additional binding sites located at some distance from the main receptor-binding domain on S1. We suggest the possibility to predict and test the short protein derived peptides for development of novel strategies in inhibiting virus infections.
Collapse
Affiliation(s)
| | - Piret Arukuusk
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Heleri Härk
- Institute of Technology, University of Tartu, Tartu, Estonia
| | | | - Mart Ustav
- Institute of Technology, University of Tartu, Tartu, Estonia.,Icosagen Cell Factory OÜ, Tartu, Estonia
| | - Ülo Langel
- Institute of Technology, University of Tartu, Tartu, Estonia.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jaak Järv
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| |
Collapse
|
9
|
Pennington LF, Gasser P, Kleinboelting S, Zhang C, Skiniotis G, Eggel A, Jardetzky TS. Directed evolution of and structural insights into antibody-mediated disruption of a stable receptor-ligand complex. Nat Commun 2021; 12:7069. [PMID: 34862384 PMCID: PMC8642555 DOI: 10.1038/s41467-021-27397-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 11/11/2021] [Indexed: 11/15/2022] Open
Abstract
Antibody drugs exert therapeutic effects via a range of mechanisms, including competitive inhibition, allosteric modulation, and immune effector mechanisms. Facilitated dissociation is an additional mechanism where antibody-mediated “disruption” of stable high-affinity macromolecular complexes can potentially enhance therapeutic efficacy. However, this mechanism is not well understood or utilized therapeutically. Here, we investigate and engineer the weak disruptive activity of an existing therapeutic antibody, omalizumab, which targets IgE antibodies to block the allergic response. We develop a yeast display approach to select for and engineer antibody disruptive efficiency and generate potent omalizumab variants that dissociate receptor-bound IgE. We determine a low resolution cryo-EM structure of a transient disruption intermediate containing the IgE-Fc, its partially dissociated receptor and an antibody inhibitor. Our results provide a conceptual framework for engineering disruptive inhibitors for other targets, insights into the failure in clinical trials of the previous high affinity omalizumab HAE variant and anti-IgE antibodies that safely and rapidly disarm allergic effector cells. Facilitated dissociation is a mechanism where antibody-mediated disruption of high-affinity complexes can enhance the therapeutic effects of a drug. Here the authors present a yeast display approach to select and engineer omalizumab variants that dissociate receptor-bound IgE to accelerate its inhibition of the allergic response.
Collapse
Affiliation(s)
- Luke F Pennington
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Progam in Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Sean N. Parker Center for Allergy Research at Stanford University, Stanford, CA, 94305, USA
| | - Pascal Gasser
- Department of Rheumatology and Immunology, University Hospital Bern, Bern, Switzerland.,Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Silke Kleinboelting
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chensong Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Georgios Skiniotis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alexander Eggel
- Department of Rheumatology and Immunology, University Hospital Bern, Bern, Switzerland.,Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Theodore S Jardetzky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Progam in Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Sean N. Parker Center for Allergy Research at Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
10
|
Neira JL, Palomino-Schätzlein M, Hurtado-Gómez E, Ortore MG, Falcó A. An N-terminal half fragment of the histidine phosphocarrier protein, HPr, is disordered but binds to HPr partners and shows antibacterial properties. Biochim Biophys Acta Gen Subj 2021; 1865:130015. [PMID: 34537288 DOI: 10.1016/j.bbagen.2021.130015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/26/2021] [Accepted: 09/15/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The phosphotransferase system (PTS) modulates the preferential use of sugars in bacteria. It is formed by a protein cascade in which the first two proteins are general (namely enzyme I, EI, and the histidine phosphocarrier protein, HPr) and the others are sugar-specific permeases; the active site of HPr is His15. The HPr kinase/phosphorylase (HPrK/P), involved in the use of carbon sources in Gram-positive, phopshorylates HPr at a serine. The regulator of sigma D protein (Rsd) also binds to HPr. We are designing specific fragments of HPr, which can be used to interfere with those protein-protein interactions (PPIs), where the intact HPr intervenes. METHODS We obtained a fragment (HPr48) comprising the first forty-eight residues of HPr. HPr48 was disordered as shown by fluorescence, far-ultraviolet (UV) circular dichroism (CD), small angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR). RESULTS Secondary structure propensities, from the assigned backbone nuclei, further support the unfolded nature of the fragment. However, HPr48 was capable of binding to: (i) the N-terminal region of EI, EIN; (ii) the intact Rsd; and, (iii) HPrK/P, as shown by fluorescence, far-UV CD, NMR and biolayer interferometry (BLI). The association constants for each protein, as measured by fluorescence and BLI, were in the order of the low micromolar range, similar to those measured between the intact HPr and each of the other macromolecules. CONCLUSIONS Although HPr48 is forty-eight-residue long, it assisted antibiotics to exert antimicrobial activity. GENERAL SIGNIFICANCE HPr48 could be used as a lead compound in the development of new antibiotics, or, alternatively, to improve the efficiency of existing ones.
Collapse
Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202, Elche (Alicante), Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | | | | | - María G Ortore
- Dipartimento DiSVA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Alberto Falcó
- IDIBE, Universidad Miguel Hernández, 03202, Elche (Alicante), Spain.
| |
Collapse
|
11
|
Spizzichino S, Boi D, Boumis G, Lucchi R, Liberati FR, Capelli D, Montanari R, Pochetti G, Piacentini R, Parisi G, Paone A, Rinaldo S, Contestabile R, Tramonti A, Paiardini A, Giardina G, Cutruzzolà F. Cytosolic localization and in vitro assembly of human de novo thymidylate synthesis complex. FEBS J 2021; 289:1625-1649. [PMID: 34694685 PMCID: PMC9299187 DOI: 10.1111/febs.16248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/21/2021] [Indexed: 11/27/2022]
Abstract
De novo thymidylate synthesis is a crucial pathway for normal and cancer cells. Deoxythymidine monophosphate (dTMP) is synthesized by the combined action of three enzymes: serine hydroxymethyltransferase (SHMT1), dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), with the latter two being targets of widely used chemotherapeutics such as antifolates and 5‐fluorouracil. These proteins translocate to the nucleus after SUMOylation and are suggested to assemble in this compartment into the thymidylate synthesis complex. We report the intracellular dynamics of the complex in cancer cells by an in situ proximity ligation assay, showing that it is also detected in the cytoplasm. This result indicates that the role of the thymidylate synthesis complex assembly may go beyond dTMP synthesis. We have successfully assembled the dTMP synthesis complex in vitro, employing tetrameric SHMT1 and a bifunctional chimeric enzyme comprising human thymidylate synthase and dihydrofolate reductase. We show that the SHMT1 tetrameric state is required for efficient complex assembly, indicating that this aggregation state is evolutionarily selected in eukaryotes to optimize protein–protein interactions. Lastly, our results regarding the activity of the complete thymidylate cycle in vitro may provide a useful tool with respect to developing drugs targeting the entire complex instead of the individual components.
Collapse
Affiliation(s)
- Sharon Spizzichino
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Dalila Boi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Giovanna Boumis
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Roberta Lucchi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Davide Capelli
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberta Montanari
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Giorgio Pochetti
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberta Piacentini
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Giacomo Parisi
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Angela Tramonti
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | | | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.,Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
| |
Collapse
|
12
|
Jia H, Aadland K, Kolaczkowski O, Kolaczkowski B. Direct molecular evidence for an ancient, conserved developmental toolkit controlling post-transcriptional gene regulation in land plants. Mol Biol Evol 2021; 38:4765-4777. [PMID: 34196710 PMCID: PMC8557471 DOI: 10.1093/molbev/msab201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In plants, miRNA production is orchestrated by a suite of proteins that control transcription of the pri-miRNA gene, post-transcriptional processing and nuclear export of the mature miRNA. Post-transcriptional processing of miRNAs is controlled by a pair of physically interacting proteins, hyponastic leaves 1 (HYL1) and Dicer-like 1 (DCL1). However, the evolutionary history and structural basis of the HYL1–DCL1 interaction is unknown. Here we use ancestral sequence reconstruction and functional characterization of ancestral HYL1 in vitro and in Arabidopsis thaliana to better understand the origin and evolution of the HYL1–DCL1 interaction and its impact on miRNA production and plant development. We found the ancestral plant HYL1 evolved high affinity for both double-stranded RNA (dsRNA) and its DCL1 partner before the divergence of mosses from seed plants (∼500 Ma), and these high-affinity interactions remained largely conserved throughout plant evolutionary history. Structural modeling and molecular binding experiments suggest that the second of two dsRNA-binding motifs (DSRMs) in HYL1 may interact tightly with the first of two C-terminal DCL1 DSRMs to mediate the HYL1–DCL1 physical interaction necessary for efficient miRNA production. Transgenic expression of the nearly 200 Ma-old ancestral flowering-plant HYL1 in A. thaliana was sufficient to rescue many key aspects of plant development disrupted by HYL1− knockout and restored near-native miRNA production, suggesting that the functional partnership of HYL1–DCL1 originated very early in and was strongly conserved throughout the evolutionary history of terrestrial plants. Overall, our results are consistent with a model in which miRNA-based gene regulation evolved as part of a conserved plant “developmental toolkit.”
Collapse
Affiliation(s)
- Haiyan Jia
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Kelsey Aadland
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA
| | - Oralia Kolaczkowski
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL
| | - Bryan Kolaczkowski
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL
| |
Collapse
|
13
|
Khodr V, Machillot P, Migliorini E, Reiser JB, Picart C. High-throughput measurements of bone morphogenetic protein/bone morphogenetic protein receptor interactions using biolayer interferometry. Biointerphases 2021; 16:031001. [PMID: 34241280 PMCID: PMC7614001 DOI: 10.1116/6.0000926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/11/2021] [Indexed: 01/03/2023] Open
Abstract
Bone morphogenetic proteins (BMPs) are an important family of growth factors playing a role in a large number of physiological and pathological processes, including bone homeostasis, tissue regeneration, and cancers. In vivo, BMPs bind successively to both BMP receptors (BMPRs) of type I and type II, and a promiscuity has been reported. In this study, we used biolayer interferometry to perform parallel real-time biosensing and to deduce the kinetic parameters (ka, kd) and the equilibrium constant (KD) for a large range of BMP/BMPR combinations in similar experimental conditions. We selected four members of the BMP family (BMP-2, 4, 7, 9) known for their physiological relevance and studied their interactions with five type-I BMP receptors (ALK1, 2, 3, 5, 6) and three type-II BMP receptors (BMPR-II, ACTR-IIA, ACTR-IIB). We reveal that BMP-2 and BMP-4 behave differently, especially regarding their kinetic interactions and affinities with the type-II BMPR. We found that BMP-7 has a higher affinity for the type-II BMPR receptor ACTR-IIA and a tenfold lower affinity with the type-I receptors. While BMP-9 has a high and similar affinity for all type-II receptors, it can interact with ALK5 and ALK2, in addition to ALK1. Interestingly, we also found that all BMPs can interact with ALK5. The interaction between BMPs and both type-I and type-II receptors in a ternary complex did not reveal further cooperativity. Our work provides a synthetic view of the interactions of these BMPs with their receptors and paves the way for future studies on their cell-type and receptor specific signaling pathways.
Collapse
Affiliation(s)
- Valia Khodr
- Interdisciplinary Research Institute of Grenoble (IRIG), ERL BRM 5000 (CNRS/UGA/CEA), CEA Grenoble, 17 rue des Martyrs, 38054 Grenoble cedex, France
- CNRS, Grenoble Institute of Technology, LMGP, UMR 5628, 3 Parvis Louis Néel, 38016 Grenoble
| | - Paul Machillot
- Interdisciplinary Research Institute of Grenoble (IRIG), ERL BRM 5000 (CNRS/UGA/CEA), CEA Grenoble, 17 rue des Martyrs, 38054 Grenoble cedex, France
- CNRS, Grenoble Institute of Technology, LMGP, UMR 5628, 3 Parvis Louis Néel, 38016 Grenoble
| | - Elisa Migliorini
- Interdisciplinary Research Institute of Grenoble (IRIG), ERL BRM 5000 (CNRS/UGA/CEA), CEA Grenoble, 17 rue des Martyrs, 38054 Grenoble cedex, France
- CNRS, Grenoble Institute of Technology, LMGP, UMR 5628, 3 Parvis Louis Néel, 38016 Grenoble
| | - Jean-Baptiste Reiser
- Institut de Biologie Structurale, UMR 5075, Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Catherine Picart
- Interdisciplinary Research Institute of Grenoble (IRIG), ERL BRM 5000 (CNRS/UGA/CEA), CEA Grenoble, 17 rue des Martyrs, 38054 Grenoble cedex, France
- CNRS, Grenoble Institute of Technology, LMGP, UMR 5628, 3 Parvis Louis Néel, 38016 Grenoble
| |
Collapse
|
14
|
Keesler DA, Slobodianuk TL, Kochelek CE, Skaer CW, Haberichter SL, Flood VH. Fibronectin binding to von Willebrand factor occurs via the A1 domain. Res Pract Thromb Haemost 2021; 5:e12534. [PMID: 34136746 PMCID: PMC8178691 DOI: 10.1002/rth2.12534] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 02/08/2021] [Accepted: 03/12/2021] [Indexed: 11/23/2022] Open
Abstract
Background Collagen interactions with von Willebrand factor (VWF) perform an important role in initiation of hemostasis. Objectives We hypothesized that in addition to collagen, other extracellular matrix (ECM) proteins such as fibronectin can bind VWF. Methods Fibronectin‐VWF interactions were measured by ELISA using both plasma‐derived and recombinant VWF–containing variants in specific domains. Inhibition was measured by antibody competition using antibodies directed against both VWF and fibronectin. Binding affinities were measured by the Octet Biosensor for fibronectin and collagen IV. Results Fibronectin was able to bind both plasma‐derived and recombinant wild‐type VWF. This interaction was inhibited by both anti‐VWF antibodies and collagen types III and IV. Several VWF A1 domain variants in the region of the collagen IV binding site also demonstrated absent fibronectin binding, as did variants with defects in high‐molecular‐weight multimers. Binding affinity testing showed fibronectin has a strong affinity for VWF, in a range similar to that of collagen IV. Fibronectin binds VWF via a restricted region of the A1 domain. This interaction requires high‐molecular‐weight multimers and is similar to that seen with vascular collagens. Conclusions Therefore, VWF would appear to be the common factor linking platelet adhesion to various ECM proteins and facilitating hemostasis under conditions of ECM exposure. ![]()
Collapse
Affiliation(s)
- Daniel A Keesler
- Department of Pediatrics Division of Hematology/Oncology Medical College of Wisconsin Milwaukee WI USA
| | | | | | - Chad W Skaer
- Blood Research Institute Versiti Wisconsin Milwaukee WI USA
| | - Sandra L Haberichter
- Department of Pediatrics Division of Hematology/Oncology Medical College of Wisconsin Milwaukee WI USA.,Blood Research Institute Versiti Wisconsin Milwaukee WI USA.,Children's Research Institute Children's Hospital of Wisconsin Milwaukee WI USA
| | - Veronica H Flood
- Department of Pediatrics Division of Hematology/Oncology Medical College of Wisconsin Milwaukee WI USA.,Blood Research Institute Versiti Wisconsin Milwaukee WI USA.,Children's Research Institute Children's Hospital of Wisconsin Milwaukee WI USA
| |
Collapse
|
15
|
von Willebrand factor binding to myosin assists in coagulation. Blood Adv 2021; 4:174-180. [PMID: 31935285 DOI: 10.1182/bloodadvances.2019000533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022] Open
Abstract
von Willebrand factor (VWF) binds to platelets and collagen as a means of facilitating coagulation at sites of injury. Recent evidence has shown that myosin can serve as a surface for thrombin generation and binds to activated factor V and factor X. We studied whether VWF can also bind myosin as a means of bringing factor VIII (FVIII) to sites of clot formation. A myosin-binding assay was developed using skeletal muscle myosin to measure VWF binding, and plasma-derived and recombinant VWF containing molecular disruptions at key VWF sites were tested. Competition assays were performed using anti-VWF antibodies. FVIII binding to myosin was measured using a chromogenic FVIII substrate. Thrombin generation was measured using a fluorogenic substrate with and without myosin. Wild-type recombinant VWF and human plasma VWF from healthy controls bound myosin, whereas plasma lacking VWF exhibited no detectable myosin binding. Binding was multimer dependent and blocked by anti-VWF A1 domain antibodies or A1 domain VWF variants. The specific residues involved in myosin binding were similar, but not identical, to those required for collagen IV binding. FVIII did not bind myosin directly, but FVIII activity was detected when VWF and FVIII were bound to myosin. Myosin enhanced thrombin generation in platelet-poor plasma, although no difference was detected with the addition of myosin to platelet-rich plasma. Myosin may help to facilitate delivery of FVIII to sites of injury and indirectly accelerate thrombin generation by providing a surface for VWF binding in the setting of trauma and myosin exposure.
Collapse
|
16
|
García-Rodríguez FM, Neira JL, Marcia M, Molina-Sánchez MD, Toro N. A group II intron-encoded protein interacts with the cellular replicative machinery through the β-sliding clamp. Nucleic Acids Res 2019; 47:7605-7617. [PMID: 31127285 PMCID: PMC6698660 DOI: 10.1093/nar/gkz468] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 12/15/2022] Open
Abstract
Group II introns are self-splicing mobile genetic retroelements. The spliced intron RNA and the intron-encoded protein (IEP) form ribonucleoprotein particles (RNPs) that recognize and invade specific DNA target sites. The IEP is a reverse transcriptase/maturase that may bear a C-terminal endonuclease domain enabling the RNP to cleave the target DNA strand to prime reverse transcription. However, some mobile introns, such as RmInt1, lack the En domain but nevertheless retrohome efficiently to transient single-stranded DNA target sites at a DNA replication fork. Their mobility is associated with host DNA replication, and they use the nascent lagging strand as a primer for reverse transcription. We searched for proteins that interact with RmInt1 RNPs and direct these RNPs to the DNA replication fork. Co-immunoprecipitation assays suggested that DnaN (the β-sliding clamp), a component of DNA polymerase III, interacts with the protein component of the RmInt1 RNP. Pulldown assays, far-western blots and biolayer interferometry supported this interaction. Peptide binding assays also identified a putative DnaN-interacting motif in the RmInt1 IEP structurally conserved in group II intron IEPs. Our results suggest that intron RNP interacts with the β-sliding clamp of the DNA replication machinery, favouring reverse splicing into the transient ssDNA at DNA replication forks.
Collapse
Affiliation(s)
- Fernando M García-Rodríguez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain
| | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 71 Avenue des Martyrs, Grenoble 38042, France
| | - María D Molina-Sánchez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain
| | - Nicolás Toro
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain
| |
Collapse
|
17
|
Luan E, Yun H, Ma M, Ratner DM, Cheung KC, Chrostowski L. Label-free biosensing with a multi-box sub-wavelength phase-shifted Bragg grating waveguide. BIOMEDICAL OPTICS EXPRESS 2019; 10:4825-4838. [PMID: 31565528 PMCID: PMC6757469 DOI: 10.1364/boe.10.004825] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/20/2019] [Accepted: 08/20/2019] [Indexed: 05/02/2023]
Abstract
Sub-wavelength grating (SWG) metamaterials have been considered to provide promising solutions in the development of next-generation photonic integrated circuits. In recent years, increasied interest has been paid to silicon photonic planar biosensors based on SWG geometries for performance enhancement. In this work, we demonstrate a highly sensitive label-free phase-shifted Bragg grating (PSBG) sensing configuration, which consists of sub-wavelength block arrays in both propagation and transverse directions. By introducing salt serial dilutions and electrostatic polymers assays, bulk and surface sensitivities of the proposed sensor are characterized, obtaining measured results up to 579.2 nm/RIU and 1914 pm/nm, respectively. Moreover, the proposed multi-box PSBG sensor presents an improved quality factor as high as ∼ 8000 , roughly 3-fold of the microring-based counterpart, which further improves the detection limit. At last, by employing a biotin-streptavidin affinity assay, the capability for small molecule monitoring is exemplified with a minimum detectable concentration of biotin down to 2.28 × 10 - 8 M .
Collapse
Affiliation(s)
- Enxiao Luan
- Department of Electrical and Computer Engineering, The University of British Columbia, 2332 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Han Yun
- Department of Electrical and Computer Engineering, The University of British Columbia, 2332 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Minglei Ma
- Department of Electrical and Computer Engineering, The University of British Columbia, 2332 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Daniel M. Ratner
- Department of Bioengineering, University of Washington, 3720 15th Ave NE Seattle, WA 98195-5061, USA
| | - Karen C. Cheung
- Department of Electrical and Computer Engineering, The University of British Columbia, 2332 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Lukas Chrostowski
- Department of Electrical and Computer Engineering, The University of British Columbia, 2332 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| |
Collapse
|
18
|
Kim DM, Yao X, Vanam RP, Marlow MS. Measuring the effects of macromolecular crowding on antibody function with biolayer interferometry. MAbs 2019; 11:1319-1330. [PMID: 31401928 PMCID: PMC6748605 DOI: 10.1080/19420862.2019.1647744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biotherapeutic proteins are commonly dosed at high concentrations into the blood, which is an inherently complex, crowded solution with substantial protein content. The effects of macromolecular crowding may lead to an appreciable level of non-specific hetero-association in this physiological environment. Therefore, developing a method to characterize the diverse consequences of non-specific interactions between proteins under such non-ideal, crowded conditions, which deviate substantially from those commonly employed for in vitro characterization, is vital to achieving a more complete picture of antibody function in a biological context. In this study, we investigated non-specific interactions between human serum albumin (HSA) and two monoclonal antibodies (mAbs) by static light scattering and determined these interactions are both ionic strength-dependent and mAb-dependent. Using biolayer interferometry (BLI), we assessed the effect of HSA on antigen binding by mAbs, demonstrating that these non-specific interactions have a functional impact on mAb:antigen interactions, particularly at low ionic strength. While this effect is mitigated at physiological ionic strength, our in vitro data support the notion that HSA in the blood may lead to non-specific interactions with mAbs in vivo, with a potential impact on their interactions with antigen. Furthermore, the BLI method offers a high-throughput advantage compared to orthogonal techniques such as analytical ultracentrifugation and is amenable to a greater variety of solution conditions compared to nuclear magnetic resonance spectroscopy. Our study demonstrates that BLI is a viable technology for examining the impact of non-specific interactions on specific biologically relevant interactions, providing a direct method to assess binding events in crowded conditions.
Collapse
Affiliation(s)
- Dorothy M Kim
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Xiao Yao
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Ram P Vanam
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Michael S Marlow
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA.,Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc ., Ridgefield , CT , USA
| |
Collapse
|
19
|
Neira JL, Díaz-García C, Prieto M, Coutinho A. The C-terminal SAM domain of p73 binds to the N terminus of MDM2. Biochim Biophys Acta Gen Subj 2019; 1863:760-770. [DOI: 10.1016/j.bbagen.2019.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 01/10/2023]
|
20
|
Voss JE, Gonzalez-Martin A, Andrabi R, Fuller RP, Murrell B, McCoy LE, Porter K, Huang D, Li W, Sok D, Le K, Briney B, Chateau M, Rogers G, Hangartner L, Feeney AJ, Nemazee D, Cannon P, Burton DR. Reprogramming the antigen specificity of B cells using genome-editing technologies. eLife 2019; 8:42995. [PMID: 30648968 PMCID: PMC6355199 DOI: 10.7554/elife.42995] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/31/2018] [Indexed: 12/17/2022] Open
Abstract
We have developed a method to introduce novel paratopes into the human antibody repertoire by modifying the immunoglobulin (Ig) genes of mature B cells directly using genome editing technologies. We used CRISPR-Cas9 in a homology directed repair strategy, to replace the heavy chain (HC) variable region in B cell lines with that from an HIV broadly neutralizing antibody (bnAb), PG9. Our strategy is designed to function in cells that have undergone VDJ recombination using any combination of variable (V), diversity (D) and joining (J) genes. The modified locus expresses PG9 HC which pairs with native light chains (LCs) resulting in the cell surface expression of HIV specific B cell receptors (BCRs). Endogenous activation-induced cytidine deaminase (AID) in engineered cells allowed for Ig class switching and generated BCR variants with improved HIV neutralizing activity. Thus, BCRs engineered in this way retain the genetic flexibility normally required for affinity maturation during adaptive immune responses. Peripheral blood derived primary B cells from three different donors were edited using this strategy. Engineered cells could bind the PG9 epitope and sequenced mRNA showed PG9 HC transcribed as several different isotypes after culture with CD40 ligand and IL-4.
Collapse
Affiliation(s)
- James E Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Alicia Gonzalez-Martin
- Department of Biochemistry, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Roberta P Fuller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, San Diego, United States.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Katelyn Porter
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Wenjuan Li
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Khoa Le
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States
| | - Morgan Chateau
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - Geoffrey Rogers
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - Lars Hangartner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Ann J Feeney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States
| | - Paula Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, United States.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, United States.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, United States
| |
Collapse
|
21
|
Jia H, Kolaczkowski O, Rolland J, Kolaczkowski B. Increased Affinity for RNA Targets Evolved Early in Animal and Plant Dicer Lineages through Different Structural Mechanisms. Mol Biol Evol 2018; 34:3047-3063. [PMID: 29106606 PMCID: PMC5850739 DOI: 10.1093/molbev/msx187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Understanding the structural basis for evolutionary changes in protein function is central to molecular evolutionary biology and can help determine the extent to which functional convergence occurs through similar or different structural mechanisms. Here, we combine ancestral sequence reconstruction with functional characterization and structural modeling to directly examine the evolution of sequence-structure-function across the early differentiation of animal and plant Dicer/DCL proteins, which perform the first molecular step in RNA interference by identifying target RNAs and processing them into short interfering products. We found that ancestral Dicer/DCL proteins evolved similar increases in RNA target affinities as they diverged independently in animal and plant lineages. In both cases, increases in RNA target affinities were associated with sequence changes that anchored the RNA’s 5′phosphate, but the structural bases for 5′phosphate recognition were different in animal versus plant lineages. These results highlight how molecular-functional evolutionary convergence can derive from the evolution of unique protein structures implementing similar biochemical mechanisms.
Collapse
Affiliation(s)
- Haiyan Jia
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Oralia Kolaczkowski
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL
| | - James Rolland
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL
| | - Bryan Kolaczkowski
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL.,Genetics Institute, University of Florida, Gainesville, FL
| |
Collapse
|
22
|
Sheng P, Fields C, Aadland K, Wei T, Kolaczkowski O, Gu T, Kolaczkowski B, Xie M. Dicer cleaves 5'-extended microRNA precursors originating from RNA polymerase II transcription start sites. Nucleic Acids Res 2018; 46:5737-5752. [PMID: 29746670 PMCID: PMC6009592 DOI: 10.1093/nar/gky306] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/01/2018] [Accepted: 04/11/2018] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are approximately 22 nucleotide (nt) long and play important roles in post-transcriptional regulation in both plants and animals. In animals, precursor (pre-) miRNAs are ∼70 nt hairpins produced by Drosha cleavage of long primary (pri-) miRNAs in the nucleus. Exportin-5 (XPO5) transports pre-miRNAs into the cytoplasm for Dicer processing. Alternatively, pre-miRNAs containing a 5' 7-methylguanine (m7G-) cap can be generated independently of Drosha and XPO5. Here we identify a class of m7G-capped pre-miRNAs with 5' extensions up to 39 nt long. The 5'-extended pre-miRNAs are transported by Exportin-1 (XPO1). Unexpectedly, a long 5' extension does not block Dicer processing. Rather, Dicer directly cleaves 5'-extended pre-miRNAs by recognizing its 3' end to produce mature 3p miRNA and extended 5p miRNA both in vivo and in vitro. The recognition of 5'-extended pre-miRNAs by the Dicer Platform-PAZ-Connector (PPC) domain can be traced back to ancestral animal Dicers, suggesting that this previously unrecognized Dicer reaction mode is evolutionarily conserved. Our work reveals additional genetic sources for small regulatory RNAs and substantiates Dicer's essential role in RNAi-based gene regulation.
Collapse
Affiliation(s)
- Peike Sheng
- Department of Biochemistry and Molecular Biology
- UF Health Cancer Center
| | | | - Kelsey Aadland
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences
| | - Tianqi Wei
- Department of Biochemistry and Molecular Biology
| | - Oralia Kolaczkowski
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences
| | - Tongjun Gu
- Interdisciplinary Center for Biotechnology Research
| | - Bryan Kolaczkowski
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology
- UF Health Cancer Center
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| |
Collapse
|
23
|
Lago S, Nadai M, Rossetto M, Richter SN. Surface Plasmon Resonance kinetic analysis of the interaction between G-quadruplex nucleic acids and an anti-G-quadruplex monoclonal antibody. Biochim Biophys Acta Gen Subj 2018; 1862:1276-1282. [PMID: 29524541 PMCID: PMC5988565 DOI: 10.1016/j.bbagen.2018.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 02/27/2018] [Accepted: 03/04/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND G-quadruplexes (G4s) are nucleic acids secondary structures formed in guanine-rich sequences. Anti-G4 antibodies represent a tool for the direct investigation of G4s in cells. Surface Plasmon Resonance (SPR) is a highly sensitive technology, suitable for assessing the affinity between biomolecules. We here aimed at improving the orientation of an anti-G4 antibody on the SPR sensor chip to optimize detection of binding antigens. METHODS SPR was employed to characterize the anti-G4 antibody interaction with G4 and non-G4 oligonucleotides. Dextran-functionalized sensor chips were used both in covalent coupling and capturing procedures. RESULTS The use of two leading molecule for orienting the antibody of interest allowed to improve its activity from completely non-functional to 65% active. The specificity of the anti-G4 antobody for G4 structures could thus be assessed with high sensitivity and reliability. CONCLUSIONS Optimization of the immobilization protocol for SPR biosensing, allowed us to determine the anti-G4 antibody affinity and specificity for G4 antigens with higher sensitivity with respect to other in vitro assays such as ELISA. Anti-G4 antibody specificity is a fundamental assumption for the future utilization of this kind of antibodies for monitoring G4s directly in cells. GENERAL SIGNIFICANCE The heterogeneous orientation of amine-coupling immobilized ligands is a general problem that often leads to partial or complete inactivation of the molecules. Here we describe a new strategy for improving ligand orientation: driving it from two sides. This principle can be virtually applied to every molecule that loses its activity or is poorly immobilized after standard coupling to the SPR chip surface.
Collapse
Affiliation(s)
- Sara Lago
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Monica Rossetto
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy.
| |
Collapse
|
24
|
Neira JL, Hornos F, Cozza C, Cámara-Artigas A, Abián O, Velázquez-Campoy A. The histidine phosphocarrier protein, HPr, binds to the highly thermostable regulator of sigma D protein, Rsd, and its isolated helical fragments. Arch Biochem Biophys 2017; 639:26-37. [PMID: 29288053 DOI: 10.1016/j.abb.2017.12.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 02/06/2023]
Abstract
The phosphotransferase system (PTS) controls the preferential use of sugars in bacteria and it is also involved in other processes, such as chemotaxis. It is formed by a protein cascade in which the first two proteins are general (namely, EI and HPr) and the others are sugar-specific permeases. The Rsd protein binds specifically to the RNA polymerase (RNAP) σ70 factor. We first characterized the conformational stability of Escherichia coli Rsd. And second, we delineated the binding regions of Streptomyces coelicolor, HPrsc, and E. coli Rsd, by using fragments derived from each protein. To that end, we used several biophysical probes, namely, fluorescence, CD, NMR, ITC and BLI. Rsd had a free energy of unfolding of 15 kcal mol-1 at 25 °C, and a thermal denaturation midpoint of 103 °C at pH 6.5. The affinity between Rsd and HPrsc was 2 μM. Interestingly enough, the isolated helical-peptides, comprising the third (RsdH3) and fourth (RsdH4) Rsd helices, also interacted with HPrsc in a specific manner, and with affinities similar to that of the whole Rsd. Moreover, the isolated peptide of HPrsc, HPr9-30, comprising the active site, His15, also was bound to intact Rsd with similar affinity. Therefore, binding between Rsd and HPrsc was modulated by the two helices H3 and H4 of Rsd, and the regions around the active site of HPrsc. This implies that specific fragments of Rsd and HPrsc can be used to interfere with other protein-protein interactions (PPIs) of each other protein.
Collapse
Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Spain.
| | - Felipe Hornos
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain
| | - Concetta Cozza
- Molecular Biophysics Laboratory, Department of Physics, University of Calabria, Rende, Italy
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería- ceiA3, Almería, Spain
| | - Olga Abián
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain; Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Spain; Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain; Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain.
| |
Collapse
|
25
|
Neira JL, Florencio FJ, Muro-Pastor MI. The isolated, twenty-three-residue-long, N-terminal region of the glutamine synthetase inactivating factor binds to its target. Biophys Chem 2017; 228:1-9. [DOI: 10.1016/j.bpc.2017.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 05/31/2017] [Accepted: 05/31/2017] [Indexed: 01/31/2023]
|
26
|
Kamat V, Rafique A. Designing binding kinetic assay on the bio-layer interferometry (BLI) biosensor to characterize antibody-antigen interactions. Anal Biochem 2017; 536:16-31. [PMID: 28802648 DOI: 10.1016/j.ab.2017.08.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 08/03/2017] [Accepted: 08/07/2017] [Indexed: 01/24/2023]
Abstract
The Octet biosensors provide a high-throughput alternative to the well-established surface plasmon resonance (SPR) and SPR imaging (SPRi) biosensors to characterize antibody-antigen interactions. However, the utility of the Octet biosensors for accurate and reproducible measurement of binding rate constants of monoclonal antibodies (mAbs) is limited due to challenges such as analyte rebinding, and mass transport limitation (MTL). This study focuses on addressing these challenges and provides experimental conditions to reliably measure kinetics of mAb-antigen interactions. The mAb capture density of less than 0.6 nm was found to be optimal to measure a wide range of binding affinities on Octet HTX biosensor. The titration kinetic and single cycle kinetic assays performed on Octet HTX generated reproducible binding kinetic parameters and correlated with the values measured on Biacore 4000 and MASS-1. Kinetic assays performed on 0.1 nm density mAb surfaces significantly reduced MTL and enabled characterization of picomolar affinity mAbs. Finally, kinetic analysis performed on 150 antibodies to 10 antigens with molecular weights ranging from 21kD to 105kD showed concordance between Octet HTX, Biacore 4000 and MASS-1 (R2 > 0.90). The data presented in this study suggest that under optimal experimental conditions, Octet biosensor is capable of generating kinetic values comparable to SPR/SPRi biosensors.
Collapse
Affiliation(s)
- Vishal Kamat
- Biomolecular HTS Center, Therapeutic Proteins, Regeneron Pharmaceuticals, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
| | - Ashique Rafique
- Biomolecular HTS Center, Therapeutic Proteins, Regeneron Pharmaceuticals, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| |
Collapse
|
27
|
Dias R, Manny A, Kolaczkowski O, Kolaczkowski B. Convergence of Domain Architecture, Structure, and Ligand Affinity in Animal and Plant RNA-Binding Proteins. Mol Biol Evol 2017; 34:1429-1444. [PMID: 28333205 PMCID: PMC5435087 DOI: 10.1093/molbev/msx090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Reconstruction of ancestral protein sequences using phylogenetic methods is a powerful technique for directly examining the evolution of molecular function. Although ancestral sequence reconstruction (ASR) is itself very efficient, downstream functional, and structural studies necessary to characterize when and how changes in molecular function occurred are often costly and time-consuming, currently limiting ASR studies to examining a relatively small number of discrete functional shifts. As a result, we have very little direct information about how molecular function evolves across large protein families. Here we develop an approach combining ASR with structure and function prediction to efficiently examine the evolution of ligand affinity across a large family of double-stranded RNA binding proteins (DRBs) spanning animals and plants. We find that the characteristic domain architecture of DRBs-consisting of 2-3 tandem double-stranded RNA binding motifs (dsrms)-arose independently in early animal and plant lineages. The affinity with which individual dsrms bind double-stranded RNA appears to have increased and decreased often across both animal and plant phylogenies, primarily through convergent structural mechanisms involving RNA-contact residues within the β1-β2 loop and a small region of α2. These studies provide some of the first direct information about how protein function evolves across large gene families and suggest that changes in molecular function may occur often and unassociated with major phylogenetic events, such as gene or domain duplications.
Collapse
Affiliation(s)
- Raquel Dias
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
| | - Austin Manny
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL
| | - Oralia Kolaczkowski
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL
| | - Bryan Kolaczkowski
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL
- Genetics Institute, University of Florida, Gainesville, FL
| |
Collapse
|
28
|
Weihrauch D, Krolikowski JG, Jones DW, Zaman T, Bamkole O, Struve J, Pagel PS, Lohr NL, Pritchard KA. Vasodilation of Isolated Vessels and the Isolation of the Extracellular Matrix of Tight-skin Mice. J Vis Exp 2017. [PMID: 28362381 DOI: 10.3791/55036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The interferon regulatory factor 5 (IRF5) is crucial for cells to determine if they respond in a pro-inflammatory or anti-inflammatory fashion. IRF5's ability to switch cells from one pathway to another is highly attractive as a therapeutic target. We designed a decoy peptide IRF5D with a molecular modeling software for designing small molecules and peptides. IRF5D inhibited IRF5, reduced alterations in extracellular matrix, and improved endothelial vasodilation in the tight-skin mouse (Tsk/+). The Kd of IRF5D for recombinant IRF5 is 3.72 ± 0.74 x 10-6 M as determined by binding experiments using biolayer interferometry experiments. Endothelial cells (EC) proliferation and apoptosis were unchanged using increasing concentrations of IRF5D (0 to 100 µg/mL, 24 h). Tsk/+ mice were treated with IRF5D (1 mg/kg/d subcutaneously, 21 d). IRF5 and ICAM expressions were decreased after IRF5D treatment. Endothelial function was improved as assessed by vasodilation of facialis arteries from Tsk/+ mice treated with IRF5D compared to Tsk/+ mice without IRF5D treatment. As a transcription factor, IRF5 traffics from the cytosol to the nucleus. Translocation was assessed by immunohistochemistry on cardiac myocytes cultured on the different cardiac extracellular matrices. IRF5D treatment of the Tsk/+ mouse resulted in a reduced number of IRF5 positive nuclei in comparison to the animals without IRF5D treatment (50 µg/mL, 24 h). These findings demonstrate the important role that IRF5 plays in inflammation and fibrosis in Tsk/+ mice.
Collapse
Affiliation(s)
| | - John G Krolikowski
- Department of Anesthesiology, Medical College of Wisconsin; Clement J. Zablocki Veterans Affairs Medical Center
| | - Deron W Jones
- Department of Surgery, Division of Pediatric Surgery, Children's Research Institute
| | - Tahniyath Zaman
- Department of Surgery, Division of Pediatric Surgery, Children's Research Institute
| | | | - Janine Struve
- Department of Orthopedic Surgery, Medical College of Wisconsin
| | - Paul S Pagel
- Deptarment of Anesthesiology, Clement J Zblocki Veteran Affairs Medical Center
| | - Nicole L Lohr
- Department of Medicine, Division of Cardiology, Medical College of Wisconsin
| | - Kirkwood A Pritchard
- Department of Surgery, Division of Pediatric Surgery, Children's Research Institute
| |
Collapse
|
29
|
Dengue Virus Infection Is through a Cooperative Interaction between a Mannose Receptor and CLEC5A on Macrophage as a Multivalent Hetero-Complex. PLoS One 2016; 11:e0166474. [PMID: 27832191 PMCID: PMC5104462 DOI: 10.1371/journal.pone.0166474] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/28/2016] [Indexed: 01/01/2023] Open
Abstract
Dengue fever is a mosquito-borne viral pandemic disease that is widespread in the tropical and subtropical areas. Dengue virus uses human mannose-binding receptor (MR) and DC-SIGN on macrophages as primary receptors, and CLEC5A as signaling receptor to sense the dengue virus invasion and then to signal and stimulate macrophages to secrete cytokines. But the interplay between MR/DC-SIGN and CLEC5A is unknown. Here we demonstrate a plausible mechanism for the interaction, i.e. MR/DC-SIGN first attracts the virus with high avidity, and the virus concurrently interacts with CLEC5A in close proximity to form a multivalent hetero-complex and facilitate CLEC5A-mediated signal transduction. Our study suggests that the cooperation between a high-avidity lectin-virus interaction and a nearby low-avidity signaling receptor provides a necessary connection between binding and signaling. Understanding this mechanism may lead to the development of a new antiviral strategy.
Collapse
|
30
|
Yang D, Singh A, Wu H, Kroe-Barrett R. Comparison of biosensor platforms in the evaluation of high affinity antibody-antigen binding kinetics. Anal Biochem 2016; 508:78-96. [DOI: 10.1016/j.ab.2016.06.024] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/15/2016] [Accepted: 06/24/2016] [Indexed: 01/22/2023]
|
31
|
Pantoja-Uceda D, Neira JL, Saelices L, Robles-Rengel R, Florencio FJ, Muro-Pastor MI, Santoro J. Dissecting the Binding between Glutamine Synthetase and Its Two Natively Unfolded Protein Inhibitors. Biochemistry 2016; 55:3370-82. [DOI: 10.1021/acs.biochem.6b00072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - José L. Neira
- Instituto
de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
- Instituto
de Biocomputación y Física de Sistemas Complejos (BIFI),
Unidad Asociada IQFR-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Lorena Saelices
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Rocío Robles-Rengel
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Francisco J. Florencio
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - M. Isabel Muro-Pastor
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Jorge Santoro
- Instituto
de Química Física Rocasolano (IQFR), CSIC, 28006 Madrid, Spain
| |
Collapse
|
32
|
Postelnek J, Neely RJ, Robbins MD, Gleason CR, Peterson JE, Piccoli SP. Development and Validation of Electrochemiluminescence Assays to Measure Free and Total sSLAMF7 in Human Serum in the Absence and Presence of Elotuzumab. AAPS JOURNAL 2016; 18:989-99. [PMID: 27116021 DOI: 10.1208/s12248-016-9912-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 03/29/2016] [Indexed: 11/30/2022]
Abstract
Elotuzumab is a first in class humanized IgG1 monoclonal antibody for the treatment of multiple myeloma (MM). Elotuzumab targets the glycoprotein signaling lymphocyte activation molecule family 7 (SLAMF7, also described as CS1 or CRACC) which is expressed on the surface of myeloma cells and a subset of immune cells, including natural killer cells. A soluble version of SLAMF7 (sSLAMF7) has also been reported in MM patients but has not been evaluated as a potential biomarker following therapeutic intervention. In order to measure serum levels of sSLAMF7, two immunoassays were developed to monitor changes in circulating sSLAMF7 before and after elotuzumab treatment. Free (drug-unbound) and total (drug-bound and unbound) electrochemiluminescence (ECL) ELISA assays were developed and validated following a fit for purpose (FFP) methodology. Both assays met analytical acceptance criteria for precision, drug interference, dilution linearity, spike recovery, parallelism, and stability. Both exhibited the range and sensitivity necessary to measure clinical samples with an LLOQ of 51.2 pg/mL and ULOQs of 160 (free) and 800 ng/mL (total). Previously described assays were unable to detect sSLAMF7 in healthy individuals. However, due to the increased sensitivity of these new assays, low but measurable sSLAMF7 levels were detected in all normal healthy sera evaluated and were significantly elevated in MM patients. Cohort statistics revealed a significant increase of circulating sSLAMF7 in MM patients versus normal controls and both significant decreases in free and increases in total levels of protein post-elotuzumab treatment.
Collapse
Affiliation(s)
- Jennifer Postelnek
- Bioanalytical Science-Biologics, Bristol-Myers Squibb, L14-03, Route 206 & Province Line Rd, Princeton, New Jersey, 08543, USA.
| | - Robert J Neely
- Bioanalytical Science-Biologics, Bristol-Myers Squibb, L14-03, Route 206 & Province Line Rd, Princeton, New Jersey, 08543, USA
| | - Michael D Robbins
- Discovery Medicine, Bristol-Myers Squibb, Route 206 & Province Line Rd, Princeton, New Jersey, 08543, USA
| | - Carol R Gleason
- Global Biometrics Science, Bristol-Myers Squibb, Route 206 & Province Line Rd, Princeton, New Jersey, 08543, USA
| | - Jon E Peterson
- Bioanalytical Science-Biologics, Bristol-Myers Squibb, L14-03, Route 206 & Province Line Rd, Princeton, New Jersey, 08543, USA
| | - Steven P Piccoli
- Bioanalytical Science-Biologics, Bristol-Myers Squibb, L14-03, Route 206 & Province Line Rd, Princeton, New Jersey, 08543, USA
| |
Collapse
|
33
|
Weihrauch D, Krolikowski JG, Jones DW, Zaman T, Bamkole O, Struve J, Pillai S, Pagel PS, Lohr NL, Pritchard KA. An IRF5 Decoy Peptide Reduces Myocardial Inflammation and Fibrosis and Improves Endothelial Cell Function in Tight-Skin Mice. PLoS One 2016; 11:e0151999. [PMID: 27050551 PMCID: PMC4822818 DOI: 10.1371/journal.pone.0151999] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/06/2016] [Indexed: 12/15/2022] Open
Abstract
Interferon regulatory factor 5 (IRF5) has been called a "master switch" for its ability to determine whether cells mount proinflammatory or anti-inflammatory responses. Accordingly, IRF5 should be an attractive target for therapeutic drug development. Here we report on the development of a novel decoy peptide inhibitor of IRF5 that decreases myocardial inflammation and improves vascular endothelial cell (EC) function in tight-skin (Tsk/+) mice. Biolayer interferometry studies showed the Kd of IRF5D for recombinant IRF5 to be 3.72 ± 0.74x10-6M. Increasing concentrations of IRF5D (0-100 μg/mL, 24h) had no significant effect on EC proliferation or apoptosis. Treatment of Tsk/+ mice with IRF5D (1mg/kg/d subcutaneously, 21d) reduced IRF5 and ICAM-1 expression and monocyte/macrophage and neutrophil counts in Tsk/+ hearts compared to expression in hearts from PBS-treated Tsk/+ mice (p<0.05). EC-dependent vasodilatation of facialis arteries isolated from PBS-treated Tsk/+ mice was reduced (~15%). IRF5D treatments (1mg/kg/d, 21d) improved vasodilatation in arteries isolated from Tsk/+ mice nearly 3-fold (~45%, p<0.05), representing nearly 83% of the vasodilatation in arteries isolated from C57Bl/6J mice (~55%). IRF5D (50μg/mL, 24h) reduced nuclear translocation of IRF5 in myocytes cultured on both Tsk/+ cardiac matrix and C57Bl/6J cardiac matrix (p<0.05). These data suggest that IRF5 plays a causal role in inflammation, fibrosis and impaired vascular EC function in Tsk/+ mice and that treatment with IRF5D effectively counters IRF5-dependent mechanisms of inflammation and fibrosis in the myocardium in these mice.
Collapse
Affiliation(s)
- Dorothee Weihrauch
- Departments of Anesthesiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- * E-mail:
| | - John G. Krolikowski
- Departments of Anesthesiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Deron W. Jones
- Department of Surgery, Division of Pediatric Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Children’s Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Tahniyath Zaman
- Department of Surgery, Division of Pediatric Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Children’s Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Omoshalewa Bamkole
- Departments of Anesthesiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Janine Struve
- Orthopedic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Savin Pillai
- Departments of Anesthesiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Paul S. Pagel
- Departments of Anesthesiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Clement J. Zablocki Veterans Affairs Medical Center, Milwaukee, Wisconsin, United States of America
| | - Nicole L. Lohr
- Department of Medicine, Division of Cardiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Kirkwood A. Pritchard
- Department of Surgery, Division of Pediatric Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Children’s Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| |
Collapse
|