1
|
Condeminas M, Macias MJ. Overcoming challenges in structural biology with integrative approaches and nanobody-derived technologies. Curr Opin Struct Biol 2024; 84:102764. [PMID: 38215529 DOI: 10.1016/j.sbi.2023.102764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/24/2023] [Accepted: 12/11/2023] [Indexed: 01/14/2024]
Abstract
A full understanding of protein structure is key to unraveling how these systems work, how mutations affect their function, and discovering new hotspots for drug discovery. Research tackling this field began with the analysis of globular proteins. In recent years, as technology has improved, research efforts have broadened their focus to include the study of multidomain proteins and the analysis of conformational variability, flexibility, and dynamic systems. Here, we have selected five recent examples that integrate complementary structural methods to provide insight into the behavior of modular, flexible, and transient contacts. We also describe the structural application of domains derived from single-chain antibodies, which are instrumental in overcoming the size limitation of cryogenic electron microscopy (cryoEM) studies. As these methods are continuously developed, they will lead to the interrogation of more complex systems, revealing how large signaling and transcriptional machines are assembled in the context of health and disease.
Collapse
Affiliation(s)
- Miriam Condeminas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac 10, Barcelona 08028, Spain; Department of Medicine and Life Sciences, Universitat Pompeu Fabra (MELIS-UPF), Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Maria J Macias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac 10, Barcelona 08028, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain.
| |
Collapse
|
2
|
Jatzlau J, Mendez PL, Altay A, Raaz L, Zhang Y, Mähr S, Sesver A, Reichenbach M, Mundlos S, Vingron M, Knaus P. Fluid shear stress-modulated chromatin accessibility reveals the mechano-dependency of endothelial SMAD1/5-mediated gene transcription. iScience 2023; 26:107405. [PMID: 37680470 PMCID: PMC10481294 DOI: 10.1016/j.isci.2023.107405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/20/2023] [Accepted: 07/12/2023] [Indexed: 09/09/2023] Open
Abstract
Bone morphogenetic protein (BMP) signaling and fluid shear stress (FSS) mediate complementary functions in vascular homeostasis and disease development. It remains to be shown whether altered chromatin accessibility downstream of BMP and FSS offers a crosstalk level to explain changes in SMAD-dependent transcription. Here, we employed ATAC-seq to analyze arterial endothelial cells stimulated with BMP9 and/or FSS. We found that BMP9-sensitive regions harbor non-palindromic GC-rich SMAD-binding elements (GGCTCC) and 69.7% of these regions become BMP-insensitive in the presence of FSS. While GATA and KLF transcription factor (TF) motifs are unique to BMP9- and FSS-sensitive regions, respectively, SOX motifs are common to both. Finally, we show that both SOX(13/18) and GATA(2/3/6) family members are directly upregulated by SMAD1/5. These findings highlight the mechano-dependency of SMAD-signaling by a sequential mechanism of first elevated pioneer TF expression, allowing subsequent chromatin opening to eventually providing accessibility to novel SMAD binding sites.
Collapse
Affiliation(s)
- Jerome Jatzlau
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Berlin-Brandenburg School for Regenerative Therapies (BSRT), 13353 Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Paul-Lennard Mendez
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- International Max-Planck Research School for Biology AND Computation (IMPRS-BAC), 14195 Berlin, Germany
| | - Aybuge Altay
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Lion Raaz
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- International Max-Planck Research School for Biology AND Computation (IMPRS-BAC), 14195 Berlin, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin, 13353 Berlin, Germany
| | - Yufei Zhang
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Sophia Mähr
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Akin Sesver
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Maria Reichenbach
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- International Max-Planck Research School for Biology AND Computation (IMPRS-BAC), 14195 Berlin, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin, 13353 Berlin, Germany
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- International Max-Planck Research School for Biology AND Computation (IMPRS-BAC), 14195 Berlin, Germany
| | - Petra Knaus
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Berlin-Brandenburg School for Regenerative Therapies (BSRT), 13353 Berlin, Germany
- International Max-Planck Research School for Biology AND Computation (IMPRS-BAC), 14195 Berlin, Germany
| |
Collapse
|
3
|
Gomes T, Martin-Malpartida P, Ruiz L, Aragón E, Cordeiro TN, Macias MJ. Conformational landscape of multidomain SMAD proteins. Comput Struct Biotechnol J 2021; 19:5210-5224. [PMID: 34630939 PMCID: PMC8479633 DOI: 10.1016/j.csbj.2021.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/21/2022] Open
Abstract
SMAD transcription factors, the main effectors of the TGFβ (transforming growth factor β) network, have a mixed architecture of globular domains and flexible linkers. Such a complicated architecture precluded the description of their full-length (FL) structure for many years. In this study, we unravel the structures of SMAD4 and SMAD2 proteins through an integrative approach combining Small-angle X-ray scattering, Nuclear Magnetic Resonance spectroscopy, X-ray, and computational modeling. We show that both proteins populate ensembles of conformations, with the globular domains tethered by disordered and flexible linkers, which defines a new dimension of regulation. The flexibility of the linkers facilitates DNA and protein binding and modulates the protein structure. Yet, SMAD4FL is monomeric, whereas SMAD2FL is in different monomer-dimer-trimer states, driven by interactions of the MH2 domains. Dimers are present regardless of the SMAD2FL activation state and concentration. Finally, we propose that SMAD2FL dimers are key building blocks for the quaternary structures of SMAD complexes.
Collapse
Affiliation(s)
- Tiago Gomes
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Pau Martin-Malpartida
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Lidia Ruiz
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Eric Aragón
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Tiago N. Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Maria J. Macias
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
- ICREA, Passeig Lluís Companys 23, Barcelona 08010, Spain
| |
Collapse
|
4
|
Zakrzewski PK. Canonical TGFβ Signaling and Its Contribution to Endometrial Cancer Development and Progression-Underestimated Target of Anticancer Strategies. J Clin Med 2021; 10:3900. [PMID: 34501347 PMCID: PMC8432036 DOI: 10.3390/jcm10173900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 02/08/2023] Open
Abstract
Endometrial cancer is one of the leading gynecological cancers diagnosed among women in their menopausal and postmenopausal age. Despite the progress in molecular biology and medicine, no efficient and powerful diagnostic and prognostic marker is dedicated to endometrial carcinogenesis. The canonical TGFβ pathway is a pleiotropic signaling cascade orchestrating a variety of cellular and molecular processes, whose alterations are responsible for carcinogenesis that originates from different tissue types. This review covers the current knowledge concerning the canonical TGFβ pathway (Smad-dependent) induced by prototypical TGFβ isoforms and the involvement of pathway alterations in the development and progression of endometrial neoplastic lesions. Since Smad-dependent signalization governs opposed cellular processes, such as growth arrest, apoptosis, tumor cells growth and differentiation, as well as angiogenesis and metastasis, TGFβ cascade may act both as a tumor suppressor or tumor promoter. However, the final effect of TGFβ signaling on endometrial cancer cells depends on the cancer disease stage. The multifunctional role of the TGFβ pathway indicates the possible utilization of alterations in the TGFβ cascade as a potential target of novel anticancer strategies.
Collapse
Affiliation(s)
- Piotr K Zakrzewski
- Department of Cytobiochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| |
Collapse
|
5
|
Refolding, purification, and characterization of constitutive-active human-Smad8 produced as inclusion bodies in ClearColi® BL21 (DE3). Protein Expr Purif 2021; 184:105878. [PMID: 33812004 DOI: 10.1016/j.pep.2021.105878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/24/2021] [Accepted: 03/27/2021] [Indexed: 11/21/2022]
Abstract
Smad8 is a transcriptional regulator that participates in the intracellular signaling pathway of the transforming growth factor-β (TGF-β) family. Full-length Smad8 is an inactive protein in the absence of ligand stimulation. The expression of a truncated version of the protein lacking the MH1 domain (cSmad8) revealed constitutive activity in genetically engineered mesenchymal stem cells and, in combination with BMP-2, exhibited a tendon cell-inducing potential. To further explore function and applicability of Smad8 in regenerative medicine recombinant production is required. Herein, we further engineered cSmad8 to include the transactivation signal (TAT) of the human immunodeficiency virus (HIV) to allow internalization into cells. TAT-hcSmad8 was produced in endotoxin-free ClearColi® BL21 (DE3), refolded from inclusion bodies (IBs) and purified by Heparin chromatography. Analysis of TAT-hcSmad8 by thermal shift assay revealed the formation of a hydrophobic core. The presence of mixed α-helixes and β-sheets, in line with theoretical models, was proven by circular dichroism. TAT-hcSmad8 was successfully internalized by C3H10T1/2 cells, where it was mainly found in the cytoplasm and partially in the nucleus. Finally, it was shown that TAT-hcSmad8 exhibited biological activity in C3H10T1/2 cells after co-stimulation with BMP-2.
Collapse
|