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Nithin C, Fornari RP, Pilla SP, Wroblewski K, Zalewski M, Madaj R, Kolinski A, Macnar JM, Kmiecik S. Exploring protein functions from structural flexibility using CABS-flex modeling. Protein Sci 2024; 33:e5090. [PMID: 39194135 PMCID: PMC11350595 DOI: 10.1002/pro.5090] [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: 02/29/2024] [Revised: 05/06/2024] [Accepted: 06/10/2024] [Indexed: 08/29/2024]
Abstract
Understanding protein function often necessitates characterizing the flexibility of protein structures. However, simulating protein flexibility poses significant challenges due to the complex dynamics of protein systems, requiring extensive computational resources and accurate modeling techniques. In response to these challenges, the CABS-flex method has been developed as an efficient modeling tool that combines coarse-grained simulations with all-atom detail. Available both as a web server and a standalone package, CABS-flex is dedicated to a wide range of users. The web server version offers an accessible interface for straightforward tasks, while the standalone command-line program is designed for advanced users, providing additional features, analytical tools, and support for handling large systems. This paper examines the application of CABS-flex across various structure-function studies, facilitating investigations into the interplay among protein structure, dynamics, and function in diverse research fields. We present an overview of the current status of the CABS-flex methodology, highlighting its recent advancements, practical applications, and forthcoming challenges.
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Affiliation(s)
- Chandran Nithin
- Biological and Chemical Research Centre, Faculty of ChemistryUniversity of WarsawWarsawPoland
| | - Rocco Peter Fornari
- Biological and Chemical Research Centre, Faculty of ChemistryUniversity of WarsawWarsawPoland
| | - Smita P. Pilla
- Biological and Chemical Research Centre, Faculty of ChemistryUniversity of WarsawWarsawPoland
| | - Karol Wroblewski
- Biological and Chemical Research Centre, Faculty of ChemistryUniversity of WarsawWarsawPoland
| | - Mateusz Zalewski
- Biological and Chemical Research Centre, Faculty of ChemistryUniversity of WarsawWarsawPoland
| | - Rafał Madaj
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of BiologyUniversity of WarsawWarsawPoland
| | - Andrzej Kolinski
- Biological and Chemical Research Centre, Faculty of ChemistryUniversity of WarsawWarsawPoland
| | - Joanna M. Macnar
- Biological and Chemical Research Centre, Faculty of ChemistryUniversity of WarsawWarsawPoland
- Present address:
Ryvu TherapeuticsCracowPoland
| | - Sebastian Kmiecik
- Biological and Chemical Research Centre, Faculty of ChemistryUniversity of WarsawWarsawPoland
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Lee SB, Abdal Dayem A, Kmiecik S, Lim KM, Seo DS, Kim HT, Kumar Biswas P, Do M, Kim DH, Cho SG. Efficient improvement of the proliferation, differentiation, and anti-arthritic capacity of mesenchymal stem cells by simply culturing on the immobilized FGF2 derived peptide, 44-ERGVVSIKGV-53. J Adv Res 2024; 62:119-141. [PMID: 37777063 PMCID: PMC11331723 DOI: 10.1016/j.jare.2023.09.041] [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: 09/06/2022] [Revised: 08/23/2023] [Accepted: 09/26/2023] [Indexed: 10/02/2023] Open
Abstract
INTRODUCTION The stem cell microenvironment has been evidenced to robustly affect its biological functions and clinical grade. Natural or synthetic growth factors, especially, are essential for modulating stem cell proliferation, metabolism, and differentiation via the interaction with specific extracellular receptors. Fibroblast growth factor-2 (FGF-2) possesses pleiotropic functions in various tissues and organs. It interacts with the FGF receptor (FGFR) and activates FGFR signaling pathways, which involve numerous biological functions, such as angiogenesis, wound healing, cell proliferation, and differentiation. OBJECTIVES Here, we aim to explore the molecular functions, mode of action, and therapeutic activity of yet undetermined function, FGF-2-derived peptide, FP2 (44-ERGVVSIKGV-53) in promoting the proliferation, differentiation, and therapeutic application of human Wharton's jelly mesenchymal stem cells (hWJ-MSCs) in comparison to other test peptides, canofin1 (FP1), hexafin2 (FP3), and canofin3 (FP4) with known functions. METHODS The immobilization of test peptides that are fused with mussel adhesive proteins (MAP) on the culture plate was carried out via EDC/NHS chemistry. Cell Proliferation assay, colony-forming unit, western blotting analysis, gene expression analysis, RNA-Seq. analysis, osteogenic, and chondrogenic differentiation capacity were applied to test the activity of the test peptides. We additionally utilized three-dimensional (3D) structural analysis and artificial intelligence (AI)-based AlphaFold2 and CABS-dock programs for receptor interaction prediction of the peptide receptor. We also verified the in vivo therapeutic capacity of FP2-cultured hWJ-MSCs using an osteoarthritis mice model. RESULTS Culture of hWJ-MSC onto an FP2-immobilized culture plate showed a significant increase in cell proliferation (n = 3; *p < 0.05, **p < 0.01) and the colony-forming unit (n = 3; *p < 0.05, **p < 0.01) compared with the test peptides. FP2 showed a significantly upregulated phosphorylation of FRS2α and FGFR1 and activated the AKT and ERK signaling pathways (n = 3; *p < 0.05, **p < 0.01, ***p < 0.001). Interestingly, we detected efficient FP2 receptor binding that was predicted using AI-based tools. Treatment with an AKT inhibitor significantly abrogated the FP2-mediated enhancement of cell differentiation (n = 3; *p < 0.05, **p < 0.01, ***p < 0.001). Intra-articular injection of FP2-cultured MSCs significantly mitigated arthritis symptoms in an osteoarthritis mouse model, as shown through the functional tests (n = 10; *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001), modulation of the expression level of the pro-inflammatory and anti-inflammatory genes, and improved osteochondral regeneration as demonstrated by tissue sections. CONCLUSION Our study identified the FGF-2-derived peptide FP2 as a promising candidate peptide to improve the therapeutic potential of hWJ-MSCs, especially in bone and cartilage regeneration.
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Affiliation(s)
- Soo Bin Lee
- Department of Stem Cell and Regenerative Biotechnology, Molecular & Cellular Reprogramming Center and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Ahmed Abdal Dayem
- Department of Stem Cell and Regenerative Biotechnology, Molecular & Cellular Reprogramming Center and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sebastian Kmiecik
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, 02-089 Warsaw, Poland
| | - Kyung Min Lim
- Department of Stem Cell and Regenerative Biotechnology, Molecular & Cellular Reprogramming Center and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; R&D Team, StemExOne Co., Ltd., 307 KU Technology Innovation Bldg, 120, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Dong Sik Seo
- Stem Cell Research Center of AMOLIFESCIENCE Co., Ltd, 91, Gimpo-daero 1950 Beon-gil, Tongjin-eup, Gimpo-si, Gyeonggi-do 10014, Republic of Korea
| | - Hyeong-Taek Kim
- Stem Cell Research Center of AMOLIFESCIENCE Co., Ltd, 91, Gimpo-daero 1950 Beon-gil, Tongjin-eup, Gimpo-si, Gyeonggi-do 10014, Republic of Korea
| | - Polash Kumar Biswas
- Department of Stem Cell and Regenerative Biotechnology, Molecular & Cellular Reprogramming Center and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Minjae Do
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205 USA
| | - Deok-Ho Kim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205 USA
| | - Ssang-Goo Cho
- Department of Stem Cell and Regenerative Biotechnology, Molecular & Cellular Reprogramming Center and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; R&D Team, StemExOne Co., Ltd., 307 KU Technology Innovation Bldg, 120, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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Wellslager B, Roberts J, Chowdhury N, Madan L, Orellana E, Yilmaz Ö. Porphyromonas gingivalis activates Heat-Shock-Protein 27 to drive a LC3C-specific probacterial form of select autophagy that is redox sensitive for intracellular bacterial survival in human gingival mucosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601539. [PMID: 39005460 PMCID: PMC11244920 DOI: 10.1101/2024.07.01.601539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Porphyromonas gingivalis , a major oral pathobiont, evades canonical host pathogen clearance in human primary gingival epithelial cells (GECs) by initiating a non-canonical variant of autophagy consisting of Microtubule-associated protein 1A/1B-light chain 3 (LC3)-rich autophagosomes, which then act as replicative niches. Simultaneously, P. gingivalis inhibits apoptosis and oxidative-stress, including extracellular-ATP (eATP)-mediated reactive-oxygen-species (ROS) production via phosphorylating Heat Shock Protein 27 (HSp27) with the bacterial nucleoside-diphosphate-kinase (Ndk). Here, we have mechanistically identified that P. gingivalis -mediated induction of HSp27 is crucial for the recruitment of the LC3 isoform, LC3C, to drive the formation of live P. gingivalis -containing Beclin1-ATG14-rich autophagosomes that are redox sensitive and non-degrading. HSp27 depletions of both infected GECs and gingiva-mimicking organotypic-culture systems resulted in the collapse of P. gingivalis -mediated autophagosomes, and abolished P. gingivalis -induced LC3C-specific autophagic-flux in a HSp27-dependent manner. Concurrently, HSp27 depletion accompanied by eATP treatment abrogated protracted Beclin 1-ATG14 partnering and decreased live intracellular P. gingivalis levels. These events were only partially restored via treatments with the antioxidant N-acetyl cysteine (NAC), which rescued the cellular redox environment independent of HSp27. Moreover, the temporal phosphorylation of HSp27 by the bacterial Ndk results in HSp27 tightly partnering with LC3C, hindering LC3C canonical cleavage, extending Beclin 1-ATG14 association, and halting canonical maturation. These findings pinpoint how HSp27 pleiotropically serves as a major platform-molecule, redox regulator, and stepwise modulator of LC3C during P. gingivalis -mediated non-canonical autophagy. Thus, our findings can determine specific molecular strategies for interfering with the host-adapted P. gingivalis ' successful mucosal colonization and oral dysbiosis.
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Hsiao MH, Miao Y, Liu Z, Schütze K, Limjunyawong N, Chien DCC, Monteiro WD, Chu LS, Morgenlander W, Jayaraman S, Jang SE, Gray JJ, Zhu H, Dong X, Steinegger M, Larman HB. Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.595990. [PMID: 38854075 PMCID: PMC11160688 DOI: 10.1101/2024.05.27.595990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Animal venoms, distinguished by their unique structural features and potent bioactivities, represent a vast and relatively untapped reservoir of therapeutic molecules. However, limitations associated with extracting or expressing large numbers of individual venoms and venom-like molecules have precluded their therapeutic evaluation via high throughput screening. Here, we developed an innovative computational approach to design a highly diverse library of animal venoms and "metavenoms". We employed programmable M13 hyperphage display to preserve critical disulfide-bonded structures for highly parallelized single-round biopanning with quantitation via high-throughput DNA sequencing. Our approach led to the discovery of Kunitz type domain containing proteins that target the human itch receptor Mas-related G protein-coupled receptor X4 (MRGPRX4), which plays a crucial role in itch perception. Deep learning-based structural homology mining identified two endogenous human homologs, tissue factor pathway inhibitor (TFPI) and serine peptidase inhibitor, Kunitz type 2 (SPINT2), which exhibit agonist-dependent potentiation of MRGPRX4. Highly multiplexed screening of animal venoms and metavenoms is therefore a promising approach to uncover new drug candidates.
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Affiliation(s)
- Meng-Hsuan Hsiao
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- These authors contributed equally to this work
| | - Yang Miao
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- These authors contributed equally to this work
| | - Zixing Liu
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biology, Zanvyl Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Konstantin Schütze
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Nathachit Limjunyawong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center of Research Excellence in Allergy and Immunology, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Daphne Chun-Che Chien
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Wayne Denis Monteiro
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Lee-Shin Chu
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - William Morgenlander
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sahana Jayaraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sung-eun Jang
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Viral Oncology Program, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - H. Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Roy A, Ray S. Traversing DNA-Protein Interactions Between Mesophilic and Thermophilic Bacteria: Implications from Their Cold Shock Response. Mol Biotechnol 2024; 66:824-844. [PMID: 36905463 DOI: 10.1007/s12033-023-00711-4] [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: 11/13/2022] [Accepted: 02/25/2023] [Indexed: 03/12/2023]
Abstract
Cold shock proteins (CSPs) are small, acidic proteins which contain a conserved nucleic acid-binding domain. These perform mRNA translation acting as "RNA chaperones" when triggered by low temperatures initiating their cold shock response. CSP- RNA interactions have been predominantly studied. Our focus will be CSP-DNA interaction examination, to analyse the diverse interaction patterns such as electrostatic, hydrogen and hydrophobic bonding in both thermophilic and mesophilic bacteria. The differences in the molecular mechanism of these contrasting bacterial proteins are studied. Computational techniques such as modelling, energy refinement, simulation and docking were operated to obtain data for comparative analysis. The thermostability factors which stabilise a thermophilic bacterium and their effect on their molecular regulation is investigated. Conformational deviation, atomic residual fluctuations, binding affinity, Electrostatic energy and Solvent Accessibility energy were determined during stimulation along with their conformational study. The study revealed that mesophilic bacteria E. coli CSP have higher binding affinity to DNA than thermophilic G. stearothermophilus. This was further evident by low conformation deviation and atomic fluctuations during simulation.
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Affiliation(s)
- Alankar Roy
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India.
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Jaeger-Honz S, Klein K, Schreiber F. Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data. J Cheminform 2024; 16:28. [PMID: 38475907 DOI: 10.1186/s13321-024-00822-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/02/2024] [Indexed: 03/14/2024] Open
Abstract
Computational methods such as molecular docking or molecular dynamics (MD) simulations have been developed to simulate and explore the interactions between biomolecules. However, the interactions obtained using these methods are difficult to analyse and evaluate. Interaction fingerprints (IFPs) have been proposed to derive interactions from static 3D coordinates and transform them into 1D bit vectors. More recently, the concept has been applied to derive IFPs from MD simulations, which adds a layer of complexity by adding the temporal motion and dynamics of a system. As a result, many IFPs are obtained from one MD simulation, resulting in a large number of individual IFPs that are difficult to analyse compared to IFPs derived from static 3D structures. Scientific contribution: We introduce a new method to systematically aggregate IFPs derived from MD simulation data. In addition, we propose visualisations to effectively analyse and compare IFPs derived from MD simulation data to account for the temporal evolution of interactions and to compare IFPs across different MD simulations. This has been implemented as a freely available Python library and can therefore be easily adopted by other researchers and to different MD simulation datasets.
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Affiliation(s)
- Sabrina Jaeger-Honz
- Department of Computer and Information Science, University of Konstanz, Universitätsstrasse 10, 78464, Constance, Germany.
| | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, Universitätsstrasse 10, 78464, Constance, Germany
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Universitätsstrasse 10, 78464, Constance, Germany
- Faculty of Information Technology, Monash University, Clayton, VIC, 3800, Australia
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7
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Badaczewska-Dawid A, Wróblewski K, Kurcinski M, Kmiecik S. Structure prediction of linear and cyclic peptides using CABS-flex. Brief Bioinform 2024; 25:bbae003. [PMID: 38305457 PMCID: PMC10836054 DOI: 10.1093/bib/bbae003] [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: 06/30/2023] [Revised: 12/08/2023] [Accepted: 12/28/2023] [Indexed: 02/03/2024] Open
Abstract
The structural modeling of peptides can be a useful aid in the discovery of new drugs and a deeper understanding of the molecular mechanisms of life. Here we present a novel multiscale protocol for the structure prediction of linear and cyclic peptides. The protocol combines two main stages: coarse-grained simulations using the CABS-flex standalone package and an all-atom reconstruction-optimization process using the Modeller program. We evaluated the protocol on a set of linear peptides and two sets of cyclic peptides, with cyclization through the backbone and disulfide bonds. A comparison with other state-of-the-art tools (APPTEST, PEP-FOLD, ESMFold and AlphaFold implementation in ColabFold) shows that for most cases, AlphaFold offers the highest resolution. However, CABS-flex is competitive, particularly when it comes to short linear peptides. As demonstrated, the protocol performance can be further improved by combination with the residue-residue contact prediction method or more efficient scoring. The protocol is included in the CABS-flex standalone package along with online documentation to aid users in predicting the structure of peptides and mini-proteins.
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Affiliation(s)
| | - Karol Wróblewski
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Mateusz Kurcinski
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Sebastian Kmiecik
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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González-Magaña A, Tascón I, Altuna-Alvarez J, Queralt-Martín M, Colautti J, Velázquez C, Zabala M, Rojas-Palomino J, Cárdenas M, Alcaraz A, Whitney JC, Ubarretxena-Belandia I, Albesa-Jové D. Structural and functional insights into the delivery of a bacterial Rhs pore-forming toxin to the membrane. Nat Commun 2023; 14:7808. [PMID: 38016939 PMCID: PMC10684867 DOI: 10.1038/s41467-023-43585-5] [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: 04/13/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
Bacterial competition is a significant driver of toxin polymorphism, which allows continual compensatory evolution between toxins and the resistance developed to overcome their activity. Bacterial Rearrangement hot spot (Rhs) proteins represent a widespread example of toxin polymorphism. Here, we present the 2.45 Å cryo-electron microscopy structure of Tse5, an Rhs protein central to Pseudomonas aeruginosa type VI secretion system-mediated bacterial competition. This structural insight, coupled with an extensive array of biophysical and genetic investigations, unravels the multifaceted functional mechanisms of Tse5. The data suggest that interfacial Tse5-membrane binding delivers its encapsulated pore-forming toxin fragment to the target bacterial membrane, where it assembles pores that cause cell depolarisation and, ultimately, bacterial death.
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Affiliation(s)
- Amaia González-Magaña
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), 48940, Leioa, Spain
- Departamento de Bioquímica y Biología Molecular, University of the Basque Country, 48940, Leioa, Spain
| | - Igor Tascón
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), 48940, Leioa, Spain
- Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Spain
| | - Jon Altuna-Alvarez
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), 48940, Leioa, Spain
| | - María Queralt-Martín
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071, Castellón, Spain
| | - Jake Colautti
- Department of Biochemistry and Biomedical Sciences, Michael DeGroote Institute for Infectious Disease Research, and David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Carmen Velázquez
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), 48940, Leioa, Spain
- Departamento de Bioquímica y Biología Molecular, University of the Basque Country, 48940, Leioa, Spain
| | - Maialen Zabala
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), 48940, Leioa, Spain
- Departamento de Bioquímica y Biología Molecular, University of the Basque Country, 48940, Leioa, Spain
| | - Jessica Rojas-Palomino
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071, Castellón, Spain
| | - Marité Cárdenas
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), 48940, Leioa, Spain
- Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Spain
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071, Castellón, Spain
| | - John C Whitney
- Department of Biochemistry and Biomedical Sciences, Michael DeGroote Institute for Infectious Disease Research, and David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Iban Ubarretxena-Belandia
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), 48940, Leioa, Spain.
- Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Spain.
| | - David Albesa-Jové
- Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), 48940, Leioa, Spain.
- Departamento de Bioquímica y Biología Molecular, University of the Basque Country, 48940, Leioa, Spain.
- Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Spain.
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Campolattano N, D'Abrosca G, Russo L, De Siena B, Della Gala M, De Chiara I, Marasco R, Goff A, Waddell SJ, Sacco M, Muscariello L. Insight into the on/off switch that regulates expression of the MSMEG-3762/63 efflux pump in Mycobacterium smegmatis. Sci Rep 2023; 13:20332. [PMID: 37989843 PMCID: PMC10663510 DOI: 10.1038/s41598-023-47695-4] [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: 06/20/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
Drug resistance is one of the most difficult challenges facing tuberculosis (TB) control. Drug efflux is among the mechanisms leading to drug resistance. In our previous studies, we partially characterized the ABC-type MSMEG-3762/63 efflux pump in Mycobacterium smegmatis, which shares high percentage of identity with the Mycobacterium tuberculosis Rv1687/86c pump. MSMEG-3762/63 was shown to have extrusion activity for rifampicin and ciprofloxacin, used in first and second-line anti-TB treatments. Moreover, we described the functional role of the TetR-like MSMEG-3765 protein as a repressor of the MSMEG_3762/63/65 operon and orthologous Rv1687/86/85c in M. tuberculosis. Here we show that the operon is upregulated in the macrophage environment, supporting a previous observation of induction triggered by acid-nitrosative stress. Expression of the efflux pump was also induced by sub-inhibitory concentrations of rifampicin or ciprofloxacin. Both these drugs also prevented the binding of the MSMEG-3765 TetR repressor protein to its operator in the MSMEG_3762/63/65 operon. The hypothesis that these two drugs might be responsible for the induction of the efflux pump operon was assessed by bioinformatics analyses. Docking studies using a structural model of the regulator MSMEG-3765 showed that both antibiotics abolished the ability of this transcriptional repressor to recognize the efflux pump operon by interacting with the homodimer at different binding sites within the same binding pocket. Reduced binding of the repressor leads to induction of the efflux pump in M. smegmatis, and reduced efficacy of these two anti-mycobacterial drugs.
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Affiliation(s)
- Nicoletta Campolattano
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Gianluca D'Abrosca
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Barbara De Siena
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Milena Della Gala
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Ida De Chiara
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Rosangela Marasco
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Aaron Goff
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Simon J Waddell
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Margherita Sacco
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Lidia Muscariello
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy.
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10
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Campero-Basaldua C, González J, García JA, Ramírez E, Hernández H, Aguirre B, Torres-Ramírez N, Márquez D, Sánchez NS, Gómez-Hernández N, Torres-Machorro AL, Riego-Ruiz L, Scazzocchio C, González A. Neo-functionalization in Saccharomyces cerevisiae: a novel Nrg1-Rtg3 chimeric transcriptional modulator is essential to maintain mitochondrial DNA integrity. ROYAL SOCIETY OPEN SCIENCE 2023; 10:231209. [PMID: 37920568 PMCID: PMC10618058 DOI: 10.1098/rsos.231209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/11/2023] [Indexed: 11/04/2023]
Abstract
In Saccharomyces cerevisiae, the transcriptional repressor Nrg1 (Negative Regulator of Glucose-repressed genes) and the β-Zip transcription factor Rtg3 (ReTroGrade regulation) mediate glucose repression and signalling from the mitochondria to the nucleus, respectively. Here, we show a novel function of these two proteins, in which alanine promotes the formation of a chimeric Nrg1/Rtg3 regulator that represses the ALT2 gene (encoding an alanine transaminase paralog of unknown function). An NRG1/NRG2 paralogous pair, resulting from a post-wide genome small-scale duplication event, is present in the Saccharomyces genus. Neo-functionalization of only one paralog resulted in the ability of Nrg1 to interact with Rtg3. Both nrg1Δ and rtg3Δ single mutant strains were unable to use ethanol and showed a typical petite (small) phenotype on glucose. Neither of the wild-type genes complemented the petite phenotype, suggesting irreversible mitochondrial DNA damage in these mutants. Neither nrg1Δ nor rtg3Δ mutant strains expressed genes encoded by any of the five polycistronic units transcribed from mitochondrial DNA in S. cerevisiae. This, and the direct measurement of the mitochondrial DNA gene complement, confirmed that irreversible damage of the mitochondrial DNA occurred in both mutant strains, which is consistent with the essential role of the chimeric Nrg1/Rtg3 regulator in mitochondrial DNA maintenance.
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Affiliation(s)
- Carlos Campero-Basaldua
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - James González
- Laboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - Janeth Alejandra García
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Edgar Ramírez
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Hugo Hernández
- Departamento de Biología, Facultad de Química, UNAM, México City, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - Beatriz Aguirre
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Nayeli Torres-Ramírez
- Laboratorio de Microscopía Electrónica Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - Dariel Márquez
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Norma Silvia Sánchez
- Departamento de Genética Molecular, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
| | - Nicolás Gómez-Hernández
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, SLP, México
| | - Ana Lilia Torres-Machorro
- Laboratorio de Biología Celular, Departamento de Investigación en Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias ‘Ismael Cosío Villegas', Tlalpan, Mexico
| | - Lina Riego-Ruiz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, SLP, México
| | - Claudio Scazzocchio
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Alicia González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, Ciudad de Mexi, México
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11
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Rami M, Shafique M, Sarma SP. Structural, Functional, and Mutational Studies of a Potent Subtilisin Inhibitor from Budgett's Frog, Lepidobatrachus laevis. Biochemistry 2023; 62:2952-2969. [PMID: 37796763 DOI: 10.1021/acs.biochem.3c00252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Subtilases play a significant role in microbial pathogen infections by degrading the host proteins. Subtilisin inhibitors are crucial in fighting against these harmful microorganisms. LL-TIL, from skin secretions of Lepidobatrachus laevis, is a cysteine-rich peptide belonging to the I8 family of inhibitors. Protease inhibitory assays demonstrated that LL-TIL acts as a slow-tight binding inhibitor of subtilisin Carlsberg and proteinase K with inhibition constants of 91 pM and 2.4 nM, respectively. The solution structures of LL-TIL and a mutant peptide reveal that they adopt a typical TIL-type fold with a canonical conformation of a reactive site loop (RSL). The structure of the LL-TIL-subtilisin complex and molecular dynamics (MD) simulations provided an in-depth view of the structural basis of inhibition. NMR relaxation data and molecular dynamics simulations indicated a rigid conformation of RSL, which does not alter significantly upon subtilisin binding. The energy calculation for subtilisin inhibition predicted Ile31 as the highest contributor to the binding energy, which was confirmed experimentally by site-directed mutagenesis. A chimeric mutant of LL-TIL broadened the inhibitory profile and attenuated subtilisin inhibition by 2 orders of magnitude. These results provide a template to engineer more specific and potent TIL-type subtilisin inhibitors.
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Affiliation(s)
- Mihir Rami
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Mohd Shafique
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Siddhartha P Sarma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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12
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Gupta J, Malik MZ, Chaturvedi M, Mishra M, Mishra SK, Grover A, Ray AK, Chaturvedi R. SARS CoV-2 spike protein variants exploit DC-SIGN/DC-SIGNR receptor for evolution and severity: an in-silico insight. Virusdisease 2023:1-19. [PMID: 37363363 PMCID: PMC10206574 DOI: 10.1007/s13337-023-00820-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/10/2023] [Indexed: 06/28/2023] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is related with the COVID-19 pandemic. Recent spike protein variations have had an effect on the transmission of the virus. In addition to ACE-2, spike proteins can employ DC-SIGN and its analogous receptor, DC-SIGNR, for host evasion. Spike variations in the DC-SIGN interaction region and role of DC-SIGN in immune evasion have not been well defined. To understand the spike protein variations and their binding mode, phylogenetic analysis of the complete GISAID (Global Initiative for Sharing Avian Influenza Data) data of the SARS-CoV-2 spike protein was considered. In addition, an in silico knockout network evaluation of the SARS-CoV-2 single-cell transcriptome was conducted to determine the key role of DC-SIGN/R in immunological dysregulation. Within the DC-SIGN-interacting region of the SARS-CoV spike protein, the spike protein of SARS-CoV-2 displayed remarkable similarity to the SARS-CoV spike protein. Surprisingly, the phylogenetic analysis revealed that the SARS-CoV-2's spike exhibited significantly diverse variants in the DC-SIGN interaction domain, which altered the frequency of these variants. The variation within the DC-SIGN-interacting domain of spike proteins affected the binding of a limited number of variants with DC-SIGN and DC-SIGNR and affected their evolution. MMGBSA binding free energies evaluation differed for variants from those of the wild type, suggesting the influence of substitution mutations on the interaction pattern. In silico knockout network analysis of the single-cell transcriptome of Bronchoalveolar Lavage and peripheral blood mononuclear cells revealed that SARS-CoV-2 altered DC-SIGN/R signaling. Early surveillance of diverse SARS-CoV-2 strains could preclude a worsening of the pandemic and facilitate the development of an optimum vaccine against variations. The spike Receptor Binding Domain genetic variants are thought to boost SARS CoV-2 immune evasion, resulting in its higher longevity. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00820-3.
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Affiliation(s)
- Jyoti Gupta
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Md. Zubbair Malik
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, 15462 Kuwait
| | - Maya Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Mohit Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Surbhi Kriti Mishra
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Ashwini Kumar Ray
- Department of Environmental Studies, University of Delhi, New Delhi, 11007 India
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
- Special Center for Systems Medicine, Jawaharlal Nehru University, New Delhi, 110067 India
- Nanofludiks Research Pvt. Ltd., JNU-Atal Incubation Center, Jawaharlal Nehru University, New Delhi, 110067 India
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13
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Alfonso-Prieto M, Capelli R. Machine Learning-Based Modeling of Olfactory Receptors in Their Inactive State: Human OR51E2 as a Case Study. J Chem Inf Model 2023; 63:2911-2917. [PMID: 37145455 DOI: 10.1021/acs.jcim.3c00380] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Atomistic-level investigation of olfactory receptors (ORs) is a challenging task due to the experimental/computational difficulties in the structural determination/prediction for members of this family of G-protein coupled receptors. Here, we have developed a protocol that performs a series of molecular dynamics simulations from a set of structures predicted de novo by recent machine learning algorithms and apply it to a well-studied receptor, the human OR51E2. Our study demonstrates the need for simulations to refine and validate such models. Furthermore, we demonstrate the need for the sodium ion at a binding site near D2.50 and E3.39 to stabilize the inactive state of the receptor. Considering the conservation of these two acidic residues across human ORs, we surmise this requirement also applies to the other ∼400 members of this family. Given the almost concurrent publication of a CryoEM structure of the same receptor in the active state, we propose this protocol as an in silico complement to the growing field of ORs structure determination.
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Affiliation(s)
- Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulation IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, D-52428 Jülich, Germany
| | - Riccardo Capelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, I-20133 Milan, Italy
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