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Tong B, Leong SG, Jian T, Niu G, Gai Y, Meng X, Lv H, Dong X, Ding X, Chen J. Site-specific pegylated IL2 mutein with biased IL2 receptor binding for cancer immunotherapy. Int Immunopharmacol 2024; 136:112359. [PMID: 38815348 DOI: 10.1016/j.intimp.2024.112359] [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: 05/06/2024] [Accepted: 05/24/2024] [Indexed: 06/01/2024]
Abstract
While Interleukin 2 (IL2) has the capability to activate both NK and T cells robustly, its limited in vivo half-life, considerable toxicity, and tendency to boost Treg cells pose significant challenges, restricting its widespread application in cancer therapy. In this investigation, we engineered a novel IL2 variant (IL2-4M-PEG) with reduced CD25 binding activity and an extended half-life by substituting amino acids associated with CD25 binding and implementing site-directed PEGylation. IL2-4M-PEG notably amplifies effector cells over Treg cells. Furthermore, our findings reveal that IL2-4M-PEG, characterized by an extended half-life, exhibits anti-tumor effects in a mouse model. Consequently, this innovative IL2 holds the potential for enhancing combined cancer therapies in the future.
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Affiliation(s)
- Bei Tong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Sirou Grace Leong
- Department of Oncology, Nanjing Drum Tower Hospital, School of Life Science, Nanjing University, Nanjing, China
| | - Tunyu Jian
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Guanting Niu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yanan Gai
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xiuhua Meng
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Han Lv
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xianchi Dong
- Department of Oncology, Nanjing Drum Tower Hospital, School of Life Science, Nanjing University, Nanjing, China; Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, China.
| | - Xiaoqin Ding
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China.
| | - Jian Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China.
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Holowinski P, Dybowski MP. Determination of 3- and 4-chloromethcathinone interactions with plasma proteins: study involving analytical and theoretical methods. Forensic Toxicol 2024; 42:111-124. [PMID: 38108940 PMCID: PMC11269353 DOI: 10.1007/s11419-023-00677-7] [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: 05/14/2023] [Accepted: 09/27/2023] [Indexed: 12/19/2023]
Abstract
PURPOSE The purpose of this paper was to determine 3- and 4-chloromethcathinone (3- and 4-CMC) binding degree and possible binding interaction modes with human serum albumin (HSA) using analytical and theoretical methods. METHODS Experimental determination of 3- and 4-CMC binding degree with HSA was performed using gas chromatography-tandem mass spectrometry preceded by the equilibrium dialysis (ED) and ultrafiltration (UF). Nuclear magnetic resonance (NMR) spectroscopy was used to determine 3- and 4-CMC epitope-binding maps and possible binding sites in HSA. The molecular docking and molecular dynamics were employed to obtain detailed information about binding modes of 3- and 4-CMC enantiomers in HSA. RESULTS As follows from the presented data, the degree of binding of 3- and 4-CMC is at a similar level of approx. 80%. This indicates a relatively strong binding of CMC to plasma proteins. The model studies employing the NMR spectroscopy and molecular simulations indicate that both CMCs bind to HSA. The whole 3- and 4-CMC molecules are embedded in the binding sites, with aromatic moieties being in the closest contact with the HSA residues. Moreover, conducted experiments show that Sudlow site II is the main binding center for 3- and 4-CMC and Sudlow site I acts as the secondary binding site. CONCLUSIONS Although many studies describe pharmacological and toxicological properties of synthetic cathinones (SC), the data taking SCs binding in plasma into consideration are scarce. To our knowledge, this is the first report presenting comprehensive experimental and theoretical characterization of 3- and 4-CMC binding with plasma proteins.
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Affiliation(s)
- Piotr Holowinski
- Faculty of Chemistry, Department of Chromatography, Institute of Chemical Sciences, Maria Curie Sklodowska University in Lublin, 20-031, Lublin, Poland
| | - Michal P Dybowski
- Faculty of Chemistry, Department of Chromatography, Institute of Chemical Sciences, Maria Curie Sklodowska University in Lublin, 20-031, Lublin, Poland.
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Franco-Mateos E, Souza-Egipsy V, García-Estévez L, Pérez-García J, Gion M, Garrigós L, Cortez P, Saavedra C, Gómez P, Ortiz C, Cruz VL, Ramos J, Cortés J, Vega JF. Exploring the Combined Action of Adding Pertuzumab to Branded Trastuzumab versus Trastuzumab Biosimilars for Treating HER2+ Breast Cancer. Int J Mol Sci 2024; 25:3940. [PMID: 38612751 PMCID: PMC11011846 DOI: 10.3390/ijms25073940] [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: 02/22/2024] [Revised: 03/18/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
The binding activity of various trastuzumab biosimilars versus the branded trastuzumab towards the glycosylated extracellular domain of the human epidermal growth factor receptor 2 (HER2) target in the presence of pertuzumab was investigated. We employed size exclusion chromatography with tetra-detection methodology to simultaneously determine absolute molecular weight, concentration, molecular size, and intrinsic viscosity. All trastuzumab molecules in solution exhibit analogous behavior in their binary action towards HER2 regardless of the order of addition of trastuzumab/pertuzumab. This analogous behavior of all trastuzumab molecules, including biosimilars, highlights the robustness and consistency of their binding activity towards HER2. Furthermore, the addition of HER2 to a mixture of trastuzumab and pertuzumab leads to increased formation of high-order HER2 complexes, up to concentrations of one order of magnitude higher than in the case of sequential addition. The observed increase suggests a potential synergistic effect between these antibodies, which could enhance their therapeutic efficacy in HER2-positive cancers. These findings underscore the importance of understanding the complex interplay between therapeutic antibodies and their target antigens, providing valuable insights for the development of more effective treatment strategies.
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Affiliation(s)
- Emma Franco-Mateos
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/Serrano 113 bis, 28006 Madrid, Spain; (E.F.-M.); (V.S.-E.); (V.L.C.); (J.R.)
| | - Virginia Souza-Egipsy
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/Serrano 113 bis, 28006 Madrid, Spain; (E.F.-M.); (V.S.-E.); (V.L.C.); (J.R.)
| | | | - José Pérez-García
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Hospital, 08017 Barcelona, Spain; (J.P.-G.); (L.G.); (P.G.); (C.O.); (J.C.)
- Medica Scientia Innovation Research (MedSIR), 08018 Barcelona, Spain
- Medica Scientia Innovation Research (MedSIR), Ridgewood, NJ 07450, USA
| | - María Gion
- Medical Oncology Department, Ramón y Cajal University Hospital, 28034 Madrid, Spain; (M.G.); (C.S.)
| | - Laia Garrigós
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Hospital, 08017 Barcelona, Spain; (J.P.-G.); (L.G.); (P.G.); (C.O.); (J.C.)
| | | | - Cristina Saavedra
- Medical Oncology Department, Ramón y Cajal University Hospital, 28034 Madrid, Spain; (M.G.); (C.S.)
| | - Patricia Gómez
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Hospital, 08017 Barcelona, Spain; (J.P.-G.); (L.G.); (P.G.); (C.O.); (J.C.)
| | - Carolina Ortiz
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Hospital, 08017 Barcelona, Spain; (J.P.-G.); (L.G.); (P.G.); (C.O.); (J.C.)
| | - Víctor L. Cruz
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/Serrano 113 bis, 28006 Madrid, Spain; (E.F.-M.); (V.S.-E.); (V.L.C.); (J.R.)
| | - Javier Ramos
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/Serrano 113 bis, 28006 Madrid, Spain; (E.F.-M.); (V.S.-E.); (V.L.C.); (J.R.)
| | - Javier Cortés
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Hospital, 08017 Barcelona, Spain; (J.P.-G.); (L.G.); (P.G.); (C.O.); (J.C.)
- Medica Scientia Innovation Research (MedSIR), 08018 Barcelona, Spain
- Faculty of Biomedical and Health Sciences, Department of Medicine, Universidad Europea de Madrid, 28670 Madrid, Spain
| | - Juan F. Vega
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/Serrano 113 bis, 28006 Madrid, Spain; (E.F.-M.); (V.S.-E.); (V.L.C.); (J.R.)
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Peter C, Schulz WA, Whongsiri P. Characterization of Native COMPASS Complex in Urothelial Carcinoma Cells by Size Exclusion Chromatography. Methods Mol Biol 2023; 2684:101-109. [PMID: 37410229 DOI: 10.1007/978-1-0716-3291-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The human COMPASS complexes regulate gene expression during development and cell differentiation. Three distinct subunits, KMT2C, KMT2D, and KDM6A (also known as UTX), are frequently mutated in urothelial carcinoma, possibly disrupting the formation of functional COMPASS complexes. Here, we describe methods to evaluate the formation of these large native protein complexes in urothelial carcinoma (UC) cell lines harboring different mutations in KMT2C/D. To this end COMPASS complexes were purified from nuclear extracts by size exclusion chromatography (SEC) using a Sepharose 6 column. SEC fractions were then separated by 3-8% Tris-acetate gradient polyacrylamide gel and the COMPASS complex subunits KMT2C, UTX, WDR5, and RBBP5 were detected by immunoblotting. In this fashion, the formation of a COMPASS complex could be observed in UC cells with wild-type but not in cells with mutant KMT2C and KMTD.
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Affiliation(s)
- Christoph Peter
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University, Düsseldorf, Germany
| | - Patcharawalai Whongsiri
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand.
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5
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Choi J, Wahlgren M, Ek V, Elofsson U, Fransson J, Nilsson L, Terry A, Söderberg CAG. Characterization of binding between model protein GA-Z and human serum albumin using asymmetrical flow field-flow fractionation and small angle X-ray scattering. PLoS One 2020; 15:e0242605. [PMID: 33232370 PMCID: PMC7685474 DOI: 10.1371/journal.pone.0242605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 11/06/2020] [Indexed: 01/01/2023] Open
Abstract
Protein-based drugs often require targeted drug delivery for optimal therapy. A successful strategy to increase the circulation time of the protein in the blood is to link the therapeutic protein with an albumin-binding domain. In this work, we characterized such a protein-based drug, GA-Z. Using asymmetrical flow field-flow fractionation coupled with multi-angle light scattering (AF4-MALS) we investigated the GA-Z monomer-dimer equilibrium as well as the molar binding ratio of GA-Z to HSA. Using small angle X-ray scattering, we studied the structure of GA-Z as well as the complex between GA-Z and HSA. The results show that GA-Z is predominantly dimeric in solution at pH 7 and that it binds to monomeric as well as dimeric HSA. Furthermore, GA-Z binds to HSA both as a monomer and a dimer, and thus, it can be expected to stay bound also upon dilution following injection in the blood stream. The results from SAXS and binding studies indicate that the GA-Z dimer is formed between two target domains (Z-domains). The results also indicate that the binding of GA-Z to HSA does not affect the ratio between HSA dimers and monomers, and that no higher order oligomers of the complex are seen other than those containing dimers of GA-Z and dimers of HSA.
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Affiliation(s)
- Jaeyeong Choi
- Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | - Marie Wahlgren
- Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | - Vilhelm Ek
- Swedish Orphan Biovitrum AB (Sobi), Stockholm, Sweden
| | - Ulla Elofsson
- Division of Bioscience and Materials, RISE Research Institutes of Sweden, Lund, Sweden
| | | | - Lars Nilsson
- Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | - Ann Terry
- MAX IV Laboratory, Lund University, Lund, Sweden
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Transient multimers modulate conformer abundances of prion protein monomer through conformational selection. Sci Rep 2019; 9:12159. [PMID: 31434938 PMCID: PMC6704068 DOI: 10.1038/s41598-019-48377-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 08/01/2019] [Indexed: 01/15/2023] Open
Abstract
Prions are known to be involved in neurodegenerative pathologies such as Creutzfeld-Jakob disease. Current models point to a molecular event which rely on a transmissible structural change that leads to the production of β-sheet-rich prion conformer (PrPSc). PrPSc itself has the capability to trigger the structural rearrangement of the ubiquitously present prion (PrPc) substrate in a self-perpetuating cascade. In this article, we demonstrate that recombinant PrPc exists in a conformational equilibrium. The conformers’ abundances were shown to be dependent on PrPc concentration through the formation of transient multimers leading to conformational selection. The study of PrPc mutants that follow dedicated oligomerization pathways demonstrated that the conformers’ relative abundances are modified, thus reinforcing the assertion that the nature of conformers’ interactions orient the oligomerization pathways. Further this result can be viewed as the “signature” of an aborted oligomerization process. This discovery sheds a new light on the possible origin of prion protein diseases, namely that a change in prion protein structure could be transmitted through the formation of transient multimers having different conformer compositions. This could explain the selection of a transient multimeric type that could be viewed as the precursor of PrPSc responsible for structural information transmission, and strain apparition.
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Woods AG, Sokolowska I, Ngounou Wetie AG, Channaveerappa D, Dupree EJ, Jayathirtha M, Aslebagh R, Wormwood KL, Darie CC. Mass Spectrometry for Proteomics-Based Investigation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:1-26. [DOI: 10.1007/978-3-030-15950-4_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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8
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Choudhary D, Kumar A, Magliery TJ, Sotomayor M. Using thermal scanning assays to test protein-protein interactions of inner-ear cadherins. PLoS One 2017; 12:e0189546. [PMID: 29261728 PMCID: PMC5736220 DOI: 10.1371/journal.pone.0189546] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/27/2017] [Indexed: 12/15/2022] Open
Abstract
Protein-protein interactions play a crucial role in biological processes such as cell-cell adhesion, immune system-pathogen interactions, and sensory perception. Understanding the structural determinants of protein-protein complex formation and obtaining quantitative estimates of their dissociation constant (KD) are essential for the study of these interactions and for the discovery of new therapeutics. At the same time, it is equally important to characterize protein-protein interactions in a high-throughput fashion. Here, we use a modified thermal scanning assay to test interactions of wild type (WT) and mutant variants of N-terminal fragments (EC1+2) of cadherin-23 and protocadherin-15, two proteins essential for inner-ear mechanotransduction. An environmentally sensitive fluorescent dye (SYPRO orange) is used to monitor melting temperature (Tm) shifts of protocadherin-15 EC1+2 (pcdh15) in the presence of increasing concentrations of cadherin-23 EC1+2 (cdh23). These Tm shifts are absent when we use proteins containing deafness-related missense mutations known to disrupt cdh23 binding to pcdh15, and are increased for some rationally designed mutants expected to enhance binding. In addition, surface plasmon resonance binding experiments were used to test if the Tm shifts correlated with changes in binding affinity. We used this approach to find a double mutation (cdh23(T15E)- pcdh15(G16D)) that enhances binding affinity of the cadherin complex by 1.98 kJ/mol, roughly two-fold that of the WT complex. We suggest that the thermal scanning methodology can be used in high-throughput format to quickly compare binding affinities (KD from nM up to 100 μM) for some heterodimeric protein complexes and to screen small molecule libraries to find protein-protein interaction inhibitors and enhancers.
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Affiliation(s)
- Deepanshu Choudhary
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Anusha Kumar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Thomas J. Magliery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
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9
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Structural Basis of Dimeric Rasip1 RA Domain Recognition of the Ras Subfamily of GTP-Binding Proteins. Structure 2016; 24:2152-2162. [PMID: 27839947 DOI: 10.1016/j.str.2016.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/04/2016] [Accepted: 10/12/2016] [Indexed: 01/20/2023]
Abstract
Ras-interacting protein 1 (Rasip1) is an endothelial-specific Rap1 and Ras effector, important for vascular development and angiogenesis. Here, we report the crystal structure of the Rasip1 RA domain (RRA) alone, revealing the basis of dimerization, and in complex with Rap1 at 2.8 Å resolution. In contrast to most RA domains, RRA formed a dimer that can bind two Rap1 (KD = 0.9 μM) or Ras (KD = 2.2 μM) molecules. We solved the Rap1-RRA complex and found that Rasip1 binds Rap1 in the Switch I region, and Rap1 binding induces few conformation changes to Rasip1 stabilizing a β strand and an unstructured loop. Our data explain how Rasip1 can act as a Rap1 and Ras effector and show that Rasip1 defines a subgroup of dimeric RA domains that could mediate cooperative binding to membrane-associated Ras superfamily members.
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10
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Woods AG, Sokolowska I, Ngounou Wetie AG, Wormwood K, Aslebagh R, Patel S, Darie CC. Mass spectrometry for proteomics-based investigation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:1-32. [PMID: 24952176 DOI: 10.1007/978-3-319-06068-2_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Within the past years, we have witnessed a great improvement in mass spectrometry (MS) and proteomics approaches in terms of instrumentation, protein fractionation, and bioinformatics. With the current technology, protein identification alone is no longer sufficient. Both scientists and clinicians want not only to identify proteins but also to identify the protein's posttranslational modifications (PTMs), protein isoforms, protein truncation, protein-protein interaction (PPI), and protein quantitation. Here, we describe the principle of MS and proteomics and strategies to identify proteins, protein's PTMs, protein isoforms, protein truncation, PPIs, and protein quantitation. We also discuss the strengths and weaknesses within this field. Finally, in our concluding remarks we assess the role of mass spectrometry and proteomics in scientific and clinical settings in the near future. This chapter provides an introduction and overview for subsequent chapters that will discuss specific MS proteomic methodologies and their application to specific medical conditions. Other chapters will also touch upon areas that expand beyond proteomics, such as lipidomics and metabolomics.
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Affiliation(s)
- Alisa G Woods
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699-5810, USA
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Deinhardt K, Darie CC. Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. Cell Mol Life Sci 2014; 71:205-28. [PMID: 23579629 PMCID: PMC11113707 DOI: 10.1007/s00018-013-1333-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 11/28/2022]
Abstract
Following the sequencing of the human genome and many other organisms, research on protein-coding genes and their functions (functional genomics) has intensified. Subsequently, with the observation that proteins are indeed the molecular effectors of most cellular processes, the discipline of proteomics was born. Clearly, proteins do not function as single entities but rather as a dynamic network of team players that have to communicate. Though genetic (yeast two-hybrid Y2H) and biochemical methods (co-immunoprecipitation Co-IP, affinity purification AP) were the methods of choice at the beginning of the study of protein-protein interactions (PPI), in more recent years there has been a shift towards proteomics-based methods and bioinformatics-based approaches. In this review, we first describe in depth PPIs and we make a strong case as to why unraveling the interactome is the next challenge in the field of proteomics. Furthermore, classical methods of investigation of PPIs and structure-based bioinformatics approaches are presented. The greatest emphasis is placed on proteomic methods, especially native techniques that were recently developed and that have been shown to be reliable. Finally, we point out the limitations of these methods and the need to set up a standard for the validation of PPI experiments.
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Affiliation(s)
- Armand G. Ngounou Wetie
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Izabela Sokolowska
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Alisa G. Woods
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Urmi Roy
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Katrin Deinhardt
- Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Southampton, SO17 1BJ UK
- Institute for Life Sciences, University of Southampton, Life Sciences Building 85, Southampton, SO17 1BJ UK
| | - Costel C. Darie
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
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12
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Gingras AR, Puzon-McLaughlin W, Ginsberg MH. The structure of the ternary complex of Krev interaction trapped 1 (KRIT1) bound to both the Rap1 GTPase and the heart of glass (HEG1) cytoplasmic tail. J Biol Chem 2013; 288:23639-49. [PMID: 23814056 PMCID: PMC3745310 DOI: 10.1074/jbc.m113.462911] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 06/19/2013] [Indexed: 12/31/2022] Open
Abstract
Loss of function mutation in Krev interaction trapped 1 (KRIT1) causes autosomal dominant familial cerebral cavernous malformations and disrupts cardiovascular development. The biological function of KRIT1 requires that its FERM (band 4.1, ezrin, radixin, moesin) domain physically interact with both the small GTPase Rap1 and the cytoplasmic tail of the Heart of glass (HEG1) membrane anchor. In this study, we show that the KRIT1 FERM domain can bind both Rap1 and HEG1 simultaneously, and we solved the crystal structure of the KRIT1-Rap1-HEG1 ternary complex. Rap1 binds on the surface of the F1 and F2 subdomains, in an interaction that leaves its Switch II region accessible to other potential effectors. HEG1 binds in a hydrophobic pocket at the KRIT1 F1 and F3 interface, and there is no overlap with the Rap1-binding site. Indeed, the affinity of KRIT1 or the KRIT1-Rap1 complex for HEG1 is comparable (Kd = 1.2 and 0.96 μm, respectively) showing that there is no competition between the two sites. Furthermore, analysis of this structure revealed a specific ionic interaction between the F2 lobe of KRIT1 and Rap1 that could explain the remarkable Rap1 specificity of KRIT1. This structural insight enabled design of KRIT1(K570I), a mutant that binds Rap1 with 8-fold lower affinity and exhibits increased binding to HRas. These data show that HEG1 can recruit the Rap1-KRIT complex to the plasma membrane where Rap1's Switch II region remains accessible and reveals an important determinant of KRIT1's specificity for Rap1.
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Affiliation(s)
- Alexandre R Gingras
- Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA.
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13
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Loo JA, Darie CC. Investigation of stable and transient protein-protein interactions: Past, present, and future. Proteomics 2013. [PMID: 23193082 DOI: 10.1002/pmic.201200328] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This article presents an overview of the literature and a review of recent advances in the analysis of stable and transient protein-protein interactions (PPIs) with a focus on their function within cells, organs, and organisms. The significance of PTMs within the PPIs is also discussed. We focus on methods to study PPIs and methods of detecting PPIs, with particular emphasis on electrophoresis-based and MS-based investigation of PPIs, including specific examples. The validation of PPIs is emphasized and the limitations of the current methods for studying stable and transient PPIs are discussed. Perspectives regarding PPIs, with focus on bioinformatics and transient PPIs are also provided.
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Affiliation(s)
- Armand G Ngounou Wetie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
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Sokolowska I, Wetie AGN, Woods AG, Darie CC. Applications of Mass Spectrometry in Proteomics. Aust J Chem 2013. [DOI: 10.1071/ch13137] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Characterisation of proteins and whole proteomes can provide a foundation to our understanding of physiological and pathological states and biological diseases or disorders. Constant development of more reliable and accurate mass spectrometry (MS) instruments and techniques has allowed for better identification and quantification of the thousands of proteins involved in basic physiological processes. Therefore, MS-based proteomics has been widely applied to the analysis of biological samples and has greatly contributed to our understanding of protein functions, interactions, and dynamics, advancing our knowledge of cellular processes as well as the physiology and pathology of the human body. This review will discuss current proteomic approaches for protein identification and characterisation, including post-translational modification (PTM) analysis and quantitative proteomics as well as investigation of protein–protein interactions (PPIs).
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Henager SH, Hale MA, Maurice NJ, Dunnington EC, Swanson CJ, Peterson MJ, Ban JJ, Culpepper DJ, Davies LD, Sanders LK, McFarland BJ. Combining different design strategies for rational affinity maturation of the MICA-NKG2D interface. Protein Sci 2012; 21:1396-402. [PMID: 22761154 DOI: 10.1002/pro.2115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 06/19/2012] [Accepted: 06/21/2012] [Indexed: 11/09/2022]
Abstract
We redesigned residues on the surface of MICA, a protein that binds the homodimeric immunoreceptor NKG2D, to increase binding affinity with a series of rational, incremental changes. A fixed-backbone RosettaDesign protocol scored a set of initial mutations, which we tested by surface plasmon resonance for thermodynamics and kinetics of NKG2D binding, both singly and in combination. We combined the best four mutations at the surface with three affinity-enhancing mutations below the binding interface found with a previous design strategy. After curating design scores with three cross-validated tests, we found a linear relationship between free energy of binding and design score, and to a lesser extent, enthalpy and design score. Multiple mutants bound with substantial subadditivity, but in at least one case full additivity was observed when combining distant mutations. Altogether, combining the best mutations from the two strategies into a septuple mutant enhanced affinity by 50-fold, to 50 nM, demonstrating a simple, effective protocol for affinity enhancement.
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Affiliation(s)
- Samuel H Henager
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, Washington 98119-1997, USA
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Peterson MJ, Snyder WK, Westerman S, McFarland BJ. Preparative Protein Production from Inclusion Bodies and Crystallization: A Seven-Week Biochemistry Sequence. JOURNAL OF CHEMICAL EDUCATION 2011; 88:986-989. [PMID: 21691428 PMCID: PMC3117595 DOI: 10.1021/ed100594h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We describe how to produce and purify proteins from E. coli inclusion bodies by adapting versatile, preparative-scale techniques to the undergraduate laboratory schedule. This seven-week sequence of experiments fits into an annual cycle of research activity in biochemistry courses. Recombinant proteins are expressed as inclusion bodies, which are collected, washed, then solubilized in urea. Stepwise dialysis to dilute urea over the course of a week produces refolded protein. Column chromatography is used to purify protein into fractions, which are then analyzed with gel electrophoresis and concentration assays. Students culminate the project by designing crystallization trials in sitting-drop trays. Student evaluation of the experience has been positive, listing 5-12 new techniques learned, which are transferrable to graduate research in academia and industry.
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Zhi L, Mans J, Paskow MJ, Brown PH, Schuck P, Jonjić S, Natarajan K, Margulies DH. Direct interaction of the mouse cytomegalovirus m152/gp40 immunoevasin with RAE-1 isoforms. Biochemistry 2010; 49:2443-53. [PMID: 20166740 DOI: 10.1021/bi902130j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cytomegaloviruses (CMVs) are ubiquitous species-specific viruses that establish acute, persistent, and latent infections. Both human and mouse CMVs encode proteins that inhibit the activation of natural killer (NK) cells by downregulating cellular ligands for the NK cell activating receptor, NKG2D. The MCMV glycoprotein m152/gp40 downregulates the surface expression of RAE-1 to prevent NK cell control in vivo. So far, it is unclear if there is a direct interaction between m152 and RAE-1 and, if so, if m152 interacts differentially with the five identified RAE-1 isoforms, which are expressed as two groups in MCMV-susceptible or -resistant mouse strains. To address these questions, we expressed and purified the extracellular domains of RAE-1 and m152 and performed size exclusion chromatography binding assays as well as analytical ultracentrifugation and isothermal titration calorimetry to characterize these interactions quantitatively. We further evaluated the role of full-length and naturally glycosylated m152 and RAE-1 in cotransfected HEK293T cells. Our results confirmed that m152 binds RAE-1 directly, relatively tightly (K(d) < 5 microM), and with 1:1 stoichiometry. The binding is quantitatively different depending on particular RAE-1 isoforms, corresponding to the susceptibility to downregulation by m152. A PLWY motif found in RAE-1beta, although contributing to its affinity for m152, does not influence the affinity of RAE-1gamma or RAE-1delta, suggesting that other differences contribute to the RAE-1-m152 interaction. Molecular modeling of the different RAE-1 isoforms suggests a potential site for the m152 interaction.
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Affiliation(s)
- Li Zhi
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-1892, USA
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