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Chauhan S, Tomar RS. Unveiling the molecular networks underlying cellular impairment in Saccharomyces cerevisiae: investigating the effects of magnesium oxide nanoparticles on cell wall integrity and endoplasmic reticulum stress response. Environ Sci Pollut Res Int 2024:10.1007/s11356-024-33265-2. [PMID: 38602634 DOI: 10.1007/s11356-024-33265-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 04/05/2024] [Indexed: 04/12/2024]
Abstract
Nanoparticles, particularly magnesium oxide nanoparticles (MgO-NPs), are increasingly utilized in various fields, yet their potential impact on cellular systems remains a topic of concern. This study aimed to comprehensively investigate the molecular mechanisms underlying MgO-NP-induced cellular impairment in Saccharomyces cerevisiae, with a focus on cell wall integrity, endoplasmic reticulum (ER) stress response, mitochondrial function, lipid metabolism, autophagy, and epigenetic alterations. MgO-NPs were synthesized through a chemical reduction method, characterized for morphology, size distribution, and elemental composition. Concentration-dependent toxicity assays were conducted to evaluate the inhibitory effect on yeast growth, accompanied by propidium iodide (PI) staining to assess membrane damage. Intracellular reactive oxygen species (ROS) accumulation was measured, and chitin synthesis, indicative of cell wall perturbation, was examined along with the expression of chitin synthesis genes. Mitochondrial function was assessed through Psd1 localization, and ER structure was analyzed using dsRed-HDEL marker. The unfolded protein response (UPR) pathway activation was monitored, and lipid droplet formation and autophagy induction were investigated. Results demonstrated a dose-dependent inhibition of yeast growth by MgO-NPs, with concomitant membrane damage and ROS accumulation. Cell wall perturbation was evidenced by increased chitin synthesis and upregulation of chitin synthesis genes. MgO-NPs impaired mitochondrial function, disrupted ER structure, and activated the UPR pathway. Lipid droplet formation and autophagy were induced, indicating cellular stress responses. Additionally, MgO-NPs exhibited differential cytotoxicity on histone mutant strains, implicating specific histone residues in cellular response to nanoparticle stress. Immunoblotting revealed alterations in histone posttranslational modifications, particularly enhanced methylation of H3K4me. This study provides comprehensive insights into the multifaceted effects of MgO-NPs on S. cerevisiae, elucidating key molecular pathways involved in nanoparticle-induced cellular impairment. Understanding these mechanisms is crucial for assessing nanoparticle toxicity and developing strategies for safer nanoparticle applications.
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Affiliation(s)
- Shraddha Chauhan
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, India.
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2
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Xu X, Yin K, Wu R. Systematic investigation of the trafficking of glycoproteins on the cell surface. Mol Cell Proteomics 2024:100761. [PMID: 38593903 DOI: 10.1016/j.mcpro.2024.100761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/30/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024] Open
Abstract
Glycoproteins located on the cell surface play a pivotal role in nearly every extracellular activity. N-glycosylation is one of the most common and important protein modifications in eukaryotic cells, and it often regulates protein folding and trafficking. Glycosylation of cell-surface proteins undergoes meticulous regulation by various enzymes in the endoplasmic reticulum (ER) and the Golgi, ensuring their proper folding and trafficking to the cell surface. However, the impacts of protein N-glycosylation, N-glycan maturity, and protein folding status on the trafficking of cell-surface glycoproteins remain to be explored. In this work, we comprehensively and site-specifically studied the trafficking of cell-surface glycoproteins in human cells. Integrating metabolic labeling, bioorthogonal chemistry, and multiplexed proteomics, we investigated 706 N-glycosylation sites on 396 cell-surface glycoproteins in monocytes, either by inhibiting protein N-glycosylation, disturbing N-glycan maturation, or perturbing protein folding in the ER. The current results reveal their distinct impacts on the trafficking of surface glycoproteins. The inhibition of protein N-glycosylation dramatically suppresses the trafficking of many cell-surface glycoproteins. The N-glycan immaturity has more substantial effects on proteins with high N-glycosylation site densities, while the perturbation of protein folding in the ER exerts a more pronounced impact on surface glycoproteins with larger sizes. Furthermore, for N-glycosylated proteins, their trafficking to the cell surface is related to the secondary structures and adjacent amino acid residues of glycosylation sites. Systematic analysis of surface glycoprotein trafficking advances our understanding of the mechanisms underlying protein secretion and surface presentation.
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Affiliation(s)
- Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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3
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Grønbæk-Thygesen M, Hartmann-Petersen R. Cellular and molecular mechanisms of aspartoacylase and its role in Canavan disease. Cell Biosci 2024; 14:45. [PMID: 38582917 PMCID: PMC10998430 DOI: 10.1186/s13578-024-01224-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/24/2024] [Indexed: 04/08/2024] Open
Abstract
Canavan disease is an autosomal recessive and lethal neurological disorder, characterized by the spongy degeneration of the white matter in the brain. The disease is caused by a deficiency of the cytosolic aspartoacylase (ASPA) enzyme, which catalyzes the hydrolysis of N-acetyl-aspartate (NAA), an abundant brain metabolite, into aspartate and acetate. On the physiological level, the mechanism of pathogenicity remains somewhat obscure, with multiple, not mutually exclusive, suggested hypotheses. At the molecular level, recent studies have shown that most disease linked ASPA gene variants lead to a structural destabilization and subsequent proteasomal degradation of the ASPA protein variants, and accordingly Canavan disease should in general be considered a protein misfolding disorder. Here, we comprehensively summarize the molecular and cell biology of ASPA, with a particular focus on disease-linked gene variants and the pathophysiology of Canavan disease. We highlight the importance of high-throughput technologies and computational prediction tools for making genotype-phenotype predictions as we await the results of ongoing trials with gene therapy for Canavan disease.
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Affiliation(s)
- Martin Grønbæk-Thygesen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200N, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200N, Copenhagen, Denmark.
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4
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Ahmad T, Alhammadi BA, Almaazmi SY, Arafa S, Blatch GL, Dutta T, Gestwicki JE, Keyzers RA, Shonhai A, Singh H. Plasmodium falciparum heat shock proteins as antimalarial drug targets: An update. Cell Stress Chaperones 2024; 29:326-337. [PMID: 38518861 PMCID: PMC10990865 DOI: 10.1016/j.cstres.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 03/24/2024] Open
Abstract
Global efforts to eradicate malaria are threatened by multiple factors, particularly the emergence of antimalarial drug resistant strains of Plasmodium falciparum. Heat shock proteins (HSPs), particularly P. falciparum HSPs (PfHSPs), represent promising drug targets due to their essential roles in parasite survival and virulence across the various life cycle stages. Despite structural similarities between human and malarial HSPs posing challenges, there is substantial evidence for subtle differences that could be exploited for selective drug targeting. This review provides an update on the potential of targeting various PfHSP families (particularly PfHSP40, PfHSP70, and PfHSP90) and their interactions within PfHSP complexes as a strategy to develop new antimalarial drugs. In addition, the need for a deeper understanding of the role of HSP complexes at the host-parasite interface is highlighted, especially heterologous partnerships between human and malarial HSPs, as this opens novel opportunities for targeting protein-protein interactions crucial for malaria parasite survival and pathogenesis.
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Affiliation(s)
- Tanveer Ahmad
- Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
| | - Bushra A Alhammadi
- Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
| | - Shaikha Y Almaazmi
- Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
| | - Sahar Arafa
- Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
| | - Gregory L Blatch
- Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates; Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa.
| | - Tanima Dutta
- Department of Diagnostic Genomics, Pathwest, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Robert A Keyzers
- Centre for Biodiscovery & School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Addmore Shonhai
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, Punjab, India
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Higdon JR, Kang J. A Thermodynamic Approach to Characterizing Monoclonal Antibody Stability in a Subcutaneous Environment. J Pharm Sci 2024:S0022-3549(24)00105-9. [PMID: 38554929 DOI: 10.1016/j.xphs.2024.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 03/23/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Affiliation(s)
- Julia R Higdon
- Department of Biology, Valdosta State University, 1500 N Patterson St., Valdosta, GA 31698, USA
| | - Jonghoon Kang
- Department of Biology, Valdosta State University, 1500 N Patterson St., Valdosta, GA 31698, USA.
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Harihar B, Saravanan KM, Gromiha MM, Selvaraj S. Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design. Mol Biotechnol 2024:10.1007/s12033-024-01119-4. [PMID: 38498284 DOI: 10.1007/s12033-024-01119-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/10/2024] [Indexed: 03/20/2024]
Abstract
Inter-residue interactions in protein structures provide valuable insights into protein folding and stability. Understanding these interactions can be helpful in many crucial applications, including rational design of therapeutic small molecules and biologics, locating functional protein sites, and predicting protein-protein and protein-ligand interactions. The process of developing machine learning models incorporating inter-residue interactions has been improved recently. This review highlights the theoretical models incorporating inter-residue interactions in predicting folding and unfolding rates of proteins. Utilizing contact maps to depict inter-residue interactions aids researchers in developing computer models for detecting remote homologs and interface residues within protein-protein complexes which, in turn, enhances our knowledge of the relationship between sequence and structure of proteins. Further, the application of contact maps derived from inter-residue interactions is highlighted in the field of drug discovery. Overall, this review presents an extensive assessment of the significant models that use inter-residue interactions to investigate folding rates, unfolding rates, remote homology, and drug development, providing potential future advancements in constructing efficient computational models in structural biology.
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Affiliation(s)
- Balasubramanian Harihar
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, 600036, India
| | - Konda Mani Saravanan
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
- Department of Biotechnology, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, 600073, India
| | - Michael M Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, 600036, India
| | - Samuel Selvaraj
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
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Cao H, Zhou X, Xu B, Hu H, Guo J, Ma Y, Wang M, Li N, Jun Z. Advances in the study of protein folding and endoplasmic reticulum-associated degradation in mammal cells. J Zhejiang Univ Sci B 2024; 25:212-232. [PMID: 38453636 PMCID: PMC10918413 DOI: 10.1631/jzus.b2300403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 08/03/2023] [Indexed: 03/09/2024]
Abstract
The endoplasmic reticulum is a key site for protein production and quality control. More than one-third of proteins are synthesized and folded into the correct three-dimensional conformation in the endoplasmic reticulum. However, during protein folding, unfolded and/or misfolded proteins are prone to occur, which may lead to endoplasmic reticulum stress. Organisms can monitor the quality of the proteins produced by endoplasmic reticulum quality control (ERQC) and endoplasmic reticulum-associated degradation (ERAD), which maintain endoplasmic reticulum protein homeostasis by degrading abnormally folded proteins. The underlying mechanisms of protein folding and ERAD in mammals have not yet been fully explored. Therefore, this paper reviews the process and function of protein folding and ERAD in mammalian cells, in order to help clinicians better understand the mechanism of ERAD and to provide a scientific reference for the treatment of diseases caused by abnormal ERAD.
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Affiliation(s)
- Hong Cao
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai 200438, China
- National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai 200433, China
| | - Xuchang Zhou
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai 200438, China
| | - Bowen Xu
- National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai 200433, China
| | - Han Hu
- National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai 200433, China
| | - Jianming Guo
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai 200438, China
| | - Yuwei Ma
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai 200438, China
| | - Miao Wang
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai 200438, China
| | - Nan Li
- National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai 200433, China.
| | - Zou Jun
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai 200438, China.
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Ferreira FC, Amaral MD, Bacalhau M, Lopes-Pacheco M. PTI-801 (posenacaftor) shares a common mechanism with VX-445 (elexacaftor) to rescue p.Phe508del-CFTR. Eur J Pharmacol 2024; 967:176390. [PMID: 38336013 DOI: 10.1016/j.ejphar.2024.176390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/05/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
The deletion of a phenylalanine at position 508 (p.Phe508del) in the CFTR anion channel is the most prevalent variant in people with Cystic Fibrosis (CF). This variant impairs folding and stability of the CF transmembrane conductance regulator (CFTR) protein, resulting in its defective trafficking and premature degradation. Over the last years, therapeutic accomplishments have been attained in developing small molecules that partially correct p.Phe508del-CFTR defects; however, the mechanism of action (MoA) of these compounds has only started to be uncovered. In this study, we employed biochemical, fluorescence microscopy, and functional assays to examine the efficacy and properties of PTI-801, a newly developed p.Phe508del-CFTR corrector. To exploit its MoA, we assessed PTI-801 effects in combination with low temperature, genetic revertants of p.Phe508del-CFTR (the in cis p.Val510Asp, p.Gly550Glu, p.Arg1070Trp, and 4RK) and other correctors. Our results demonstrated that PTI-801 rescues p.Phe508del-CFTR processing, PM trafficking, and channel function (upon agonist stimulation) with greater correction effects in combination with ABBV-2222, FDL-169, VX-661, or VX-809, but not with VX-445. Although PTI-801 exhibited no potentiator activity on low temperature- and corrector-rescued p.Phe508del-CFTR, this compound displayed similar behavior to that of VX-445 on genetic revertants. Such evidence associated with the lack of additivity when PTI-801 and VX-445 were combined indicates that they share a common binding site to correct p.Phe508del-CFTR defects. Despite the high efficacy of PTI-801 in combination with ABBV-2222, FDL-169, VX-661, or VX-809, these dual corrector combinations only partially restored p.Phe508del-CFTR conformational stability, as shown by the lower half-life of the mutant protein compared to that of WT-CFTR. In summary, PTI-801 likely shares a common MoA with VX-445 in rescuing p.Phe508del-CFTR, thus being a feasible alternative for the development of novel corrector combinations with greater capacity to rescue mutant CFTR folding and stability.
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Affiliation(s)
- Filipa C Ferreira
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Margarida D Amaral
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Mafalda Bacalhau
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal.
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Kim H, Park J, Roh SH. The structural basis of eukaryotic chaperonin TRiC/CCT: Action and folding. Mol Cells 2024; 47:100012. [PMID: 38280673 PMCID: PMC11004407 DOI: 10.1016/j.mocell.2024.100012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/29/2024] Open
Abstract
Accurate folding of proteins in living cells often requires the cooperative support of molecular chaperones. Eukaryotic group II chaperonin Tailless complex polypeptide 1-Ring Complex (TRiC) accomplishes this task by providing a folding chamber for the substrate that is regulated by an Adenosine triphosphate (ATP) hydrolysis-dependent cycle. Once delivered to and recognized by TRiC, the nascent substrate enters the folding chamber and undergoes folding and release in a stepwise manner. During the process, TRiC subunits and cochaperones such as prefoldin and phosducin-like proteins interact with the substrate to assist the overall folding process in a substrate-specific manner. Coevolution between the components is supposed to consult the binding specificity and ultimately expand the substrate repertoire assisted by the chaperone network. This review describes the TRiC chaperonin and the substrate folding process guided by the TRiC network in cooperation with cochaperones, specifically focusing on recent progress in structural analyses.
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Affiliation(s)
- Hyunmin Kim
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Junsun Park
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Soung-Hun Roh
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea.
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da Silva FB, Simien JM, Viegas RG, Haglund E, Leite VBP. Exploring the folding landscape of leptin: Insights into threading pathways. J Struct Biol 2024; 216:108054. [PMID: 38065428 DOI: 10.1016/j.jsb.2023.108054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
The discovery of new protein topologies with entanglements and loop-crossings have shown the impact of local amino acid arrangement and global three-dimensional structures. This phenomenon plays a crucial role in understanding how protein structure relates to folding and function, affecting the global stability, and biological activity. Protein entanglements encompassing knots and non-trivial topologies add complexity to their folding free energy landscapes. However, the initial native contacts driving the threading event for entangled proteins remains elusive. The Pierced Lasso Topology (PLT) represents an entangled topology where a covalent linker creates a loop in which the polypeptide backbone is threaded through. Compared to true knotted topologies, PLTs are simpler topologies where the covalent-loop persists in all conformations. In this work, the PLT protein leptin, is used to visualize and differentiate the preference for slipknotting over plugging transition pathways along the folding route. We utilize the Energy Landscape Visualization Method (ELViM), a multidimensional projection technique, to visualize and distinguish early threaded conformations that cannot be observed in an in vitro experiment. Critical contacts for the leptin threading mechanisms were identified where the competing pathways are determined by the formation of a hairpin loop in the unfolded basin. Thus, prohibiting the dominant slipknotting pathway. Furthermore, ELViM offers insights into distinct folding pathways associated with slipknotting and plugging providing a novel tool for de novo design and in vitro experiments with residue specific information of threading events in silico.
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Affiliation(s)
- Fernando Bruno da Silva
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland; Institute of Biosciences, Humanities and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil
| | - Jennifer M Simien
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Rafael G Viegas
- Institute of Biosciences, Humanities and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil; Federal Institute of Education, Science and Technology of São Paulo (IFSP), Catanduva, SP 15.808-305, Brazil
| | - Ellinor Haglund
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States.
| | - Vitor Barbanti Pereira Leite
- Institute of Biosciences, Humanities and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil.
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Tiwari VP, De D, Thapliyal N, Kay LE, Vallurupalli P. Beyond slow two-state protein conformational exchange using CEST: applications to three-state protein interconversion on the millisecond timescale. J Biomol NMR 2024; 78:39-60. [PMID: 38169015 DOI: 10.1007/s10858-023-00431-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/15/2023] [Indexed: 01/05/2024]
Abstract
Although NMR spectroscopy is routinely used to study the conformational dynamics of biomolecules, robust analyses of the data are challenged in cases where exchange is more complex than two-state, such as when a 'visible' major conformer exchanges with two 'invisible' minor states on the millisecond timescale. It is becoming increasingly clear that chemical exchange saturation transfer (CEST) NMR experiments that were initially developed to study systems undergoing slow interconversion are also sensitive to intermediate-fast timescale biomolecular conformational exchange. Here we investigate the utility of the amide 15N CEST experiment to characterise protein three-state exchange occurring on the millisecond timescale by studying the interconversion between the folded (F) state of the FF domain from human HYPA/FBP11 (WT FF) and two of its folding intermediates I1 and I2. Although 15N CPMG experiments are consistent with the F state interconverting with a single minor state on the millisecond timescale, 15N CEST data clearly establish an exchange process between F and a pair of minor states. A unique three-state exchange model cannot be obtained by analysis of 15N CEST data recorded at a single temperature. However, including the relative sign of the difference in the chemical shifts of the two minor states based on a simple two-state analysis of CEST data recorded at multiple temperatures, results in a robust three-state model in which the F, I1 and I2 states interconvert with each other on the millisecond timescale ( k e x , F I 1 ~ 550 s-1, k e x , F I 2 ~ 1200 s-1, k e x , I 1 I 2 ~ 5000 s-1), with I1 and I2 sparsely populated at ~ 0.15% and ~ 0.35%, respectively, at 15 °C. A computationally demanding grid-search of exchange parameter space is not required to extract the best-fit exchange parameters from the CEST data. The utility of the CEST experiment, thus, extends well beyond studies of conformers in slow exchange on the NMR chemical shift timescale, to include systems with interconversion rates on the order of thousands/second.
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Affiliation(s)
- Ved Prakash Tiwari
- Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500046, India
| | - Debajyoti De
- Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500046, India
| | - Nemika Thapliyal
- Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500046, India
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Pramodh Vallurupalli
- Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500046, India.
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12
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Guan J, Jakob U. The Protein Scaffolding Functions of Polyphosphate. J Mol Biol 2024:168504. [PMID: 38423453 DOI: 10.1016/j.jmb.2024.168504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
Inorganic polyphosphate (polyP), one of the first high-energy compound on earth, defies its extreme compositional and structural simplicity with an astoundingly wide array of biological activities across all domains of life. However, the underlying mechanism of such functional pleiotropy remains largely elusive. In this review, we will summarize recent studies demonstrating that this simple polyanion stabilizes protein folding intermediates and scaffolds select native proteins. These functions allow polyP to act as molecular chaperone that protects cells against protein aggregation, as pro-amyloidogenic factor that accelerates both physiological and disease-associated amyloid formation, and as a modulator of liquid-liquid phase separation processes. These activities help to explain polyP's known roles in bacterial stress responses and pathogenicity, provide the mechanistic foundation for its potential role in human neurodegenerative diseases, and open a new direction regarding its influence on gene expression through condensate formation. We will highlight critical unanswered questions and point out potential directions that will help to further understand the pleiotropic functions of this ancient and ubiquitous biopolymer.
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Affiliation(s)
- Jian Guan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA; Biological Chemistry Department, University of Michigan Medical School, Ann Arbor, MI, USA.
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13
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Tapia-Rojo R. Construction and operation of high-resolution magnetic tape head tweezers for measuring single-protein dynamics under force. Methods Enzymol 2024; 694:83-107. [PMID: 38492959 DOI: 10.1016/bs.mie.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
Mechanical forces are critical to protein function across many biological contexts-from bacterial adhesion to muscle mechanics and mechanotransduction processes. Hence, understanding how mechanical forces govern protein activity has developed into a central scientific question. In this context, single-molecule magnetic tweezers has recently emerged as a valuable experimental tool, offering the capability to measure single proteins over physiologically relevant forces and timescales. In this chapter, we present a detailed protocol for the assembly and operation of our magnetic tape head tweezers instrument, specifically tailored to investigate protein dynamics. Our instrument boasts a simplified microscope design and incorporates a magnetic tape head as the force-generating apparatus, facilitating precise force control and enhancing its temporal stability, enabling the study of single protein mechanics over extended timescales spanning several hours or even days. Moreover, its straightforward and cost-effective design ensures its accessibility to the wider scientific community. We anticipate that this technique will attract widespread interest within the growing field of mechanobiology and expect that this chapter will provide facilitated accessibility to this technology.
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14
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Joseph J, Spantzel L, Ali M, Moonnukandathil Joseph D, Unger S, Reglinski K, Krafft C, Müller AD, Eggeling C, Heintzmann R, Börsch M, Press AT, Täuber D. Nanoscale chemical characterization of secondary protein structure of F-Actin using mid-infrared photoinduced force microscopy (PiF-IR). Spectrochim Acta A Mol Biomol Spectrosc 2024; 306:123612. [PMID: 37931494 DOI: 10.1016/j.saa.2023.123612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/15/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]
Abstract
The recently developed photoinduced force microscopy for mid-infrared (PiF-IR) offers high spectral resolution in combination with surface sensitivity and a spatial resolution in the range of a few nanometers. Although PiF-IR has primarily been applied to polymer materials, this technology presents significant potential for the chemical characterization of cellular structures approaching single-molecule sensitivity. We applied PiF-IR to differently polymerized F-Actin samples finding general agreement with FTIR spectra from the same samples. Single PiF-IR spectra of F-Actin show variations in the amide I band spectral region, which is related to secondary protein structure. Local variations are also seen in PiF-IR hyperspectra in this region. Such high sensitivity is a necessary requirement for discriminating Actin organization into bundles and other networks in cells and tissue. We applied PiF-IR to mouse liver tissue ex vivo. Single-frequency PiF-IR scans at three different IR frequencies show significant variations in local contrast. However, the presence of other proteins and the unique spatial resolution of PiF-IR pose a challenge to interpreting and validating such data. Careful design of model systems and further theoretical understanding of PiF-IR data far from bulk averages are needed to fully unfold the potential of PiF-IR for high-resolution chemical investigation in the Life Sciences.
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Affiliation(s)
- Jesvin Joseph
- Leibniz Institute of Photonic Technology, Department of Microscopy, Jena, Germany; Friedrich Schiller University Jena, Institute of Physical Chemistry & Abbe Center of Photonics, Jena, Germany
| | - Lukas Spantzel
- Jena University Hospital, Single-Molecule Microscopy Group, Jena, Germany; Friedrich Schiller University Jena, Faculty of Medicine, Jena, Germany
| | - Maryam Ali
- Friedrich Schiller University Jena, Institute of Physical Chemistry & Abbe Center of Photonics, Jena, Germany
| | - Dijo Moonnukandathil Joseph
- Leibniz Institute of Photonic Technology, Department of Microscopy, Jena, Germany; Friedrich Schiller University Jena, Institute of Physical Chemistry & Abbe Center of Photonics, Jena, Germany
| | - Sebastian Unger
- Leibniz Institute of Photonic Technology, Department of Microscopy, Jena, Germany; Friedrich Schiller University Jena, Institute of Physical Chemistry & Abbe Center of Photonics, Jena, Germany
| | - Katharina Reglinski
- Leibniz Institute of Photonic Technology, Biophysical Imaging, Jena, Germany; Friedrich Schiller University Jena, Institute for Applied Optics and Biophysics, Jena, Germany
| | - Christoph Krafft
- Leibniz Institute of Photonic Technology, Department of Spectroscopy & Imaging, Jena, Germany
| | | | - Christian Eggeling
- Leibniz Institute of Photonic Technology, Biophysical Imaging, Jena, Germany; Friedrich Schiller University Jena, Institute for Applied Optics and Biophysics, Jena, Germany
| | - Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Department of Microscopy, Jena, Germany; Friedrich Schiller University Jena, Institute of Physical Chemistry & Abbe Center of Photonics, Jena, Germany
| | - Michael Börsch
- Jena University Hospital, Single-Molecule Microscopy Group, Jena, Germany; Friedrich Schiller University Jena, Faculty of Medicine, Jena, Germany
| | - Adrian T Press
- Friedrich Schiller University Jena, Faculty of Medicine, Jena, Germany; Jena University Hospital, Department of Anesthesiology and Intensive Care Medicine, Jena, Germany
| | - Daniela Täuber
- Leibniz Institute of Photonic Technology, Department of Microscopy, Jena, Germany; Friedrich Schiller University Jena, Institute of Physical Chemistry & Abbe Center of Photonics, Jena, Germany; Friedrich Schiller University Jena, Institute of Solid State Physics, Jena, Germany.
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15
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Melki R. Disease Mechanisms of Multiple System Atrophy: What a Parallel Between the Form of Pasta and the Alpha-Synuclein Assemblies Involved in MSA and PD Tells Us. Cerebellum 2024; 23:13-21. [PMID: 35657577 PMCID: PMC10864476 DOI: 10.1007/s12311-022-01417-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Intracellular deposits rich in aggregated alpha-synuclein that appear within the central nervous system are intimately associated to Parkinson's disease and multiple system atrophy. While it is understandable that the aggregation of proteins, which share no primary structure identity, such as alpha-synuclein and tau protein, leads to different diseases, that of a given protein yielding distinct pathologies is counterintuitive. This short review relates molecular and mechanistic processes to the observed pathological diversity associated to alpha-synuclein aggregation.
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Affiliation(s)
- Ronald Melki
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, 18 Route du Panorama, 92265, Fontenay-Aux-Roses, France.
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16
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Bhatia S, Udgaonkar JB. Understanding the heterogeneity intrinsic to protein folding. Curr Opin Struct Biol 2024; 84:102738. [PMID: 38041993 DOI: 10.1016/j.sbi.2023.102738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 12/04/2023]
Abstract
Relating the native fold of a protein to its amino acid sequence remains a fundamental problem in biology. While computer algorithms have demonstrated recently their prowess in predicting what structure a particular amino acid sequence will fold to, an understanding of how and why a specific protein fold is achieved remains elusive. A major challenge is to define the role of conformational heterogeneity during protein folding. Recent experimental studies, utilizing time-resolved FRET, hydrogen-exchange coupled to mass spectrometry, and single-molecule force spectroscopy, often in conjunction with simulation, have begun to reveal how conformational heterogeneity evolves during folding, and whether an intermediate ensemble of defined free energy consists of different sub-populations of molecules that may differ significantly in conformation, energy and entropy.
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Affiliation(s)
- Sandhya Bhatia
- Department of Biophysics, Howard Hughes Medical Institute UT Southwestern Medical Center, Dallas 75390, United States. https://twitter.com/Sandhyabhatia_5
| | - Jayant B Udgaonkar
- Department of Biology, Indian Institute of Science Education and Research Pune, Pashan, Pune 41008, India.
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17
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Chen Z, Wang S, Pottekat A, Duffey A, Jang I, Chang BH, Cho J, Finck BN, Davidson NO, Kaufman RJ. Conditional hepatocyte ablation of PDIA1 uncovers indispensable roles in both APOB and MTTP folding to support VLDL secretion. Mol Metab 2024; 80:101874. [PMID: 38211723 PMCID: PMC10832468 DOI: 10.1016/j.molmet.2024.101874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/13/2024] Open
Abstract
OBJECTIVES The assembly and secretion of hepatic very low-density lipoprotein (VLDL) plays pivotal roles in hepatic and plasma lipid homeostasis. Protein disulfide isomerase A1 (PDIA1/P4HB) is a molecular chaperone whose functions are essential for protein folding in the endoplasmic reticulum. Here we investigated the physiological requirement in vivo for PDIA1 in maintaining VLDL assembly and secretion. METHODS Pdia1/P4hb was conditionally deleted in adult mouse hepatocytes and the phenotypes characterized. Mechanistic analyses in primary hepatocytes determined how PDIA1 ablation alters MTTP synthesis and degradation as well as altering synthesis and secretion of Apolipoprotein B (APOB), along with complementary expression of intact PDIA1 vs a catalytically inactivated PDIA1 mutant. RESULTS Hepatocyte-specific deletion of Pdia1/P4hb inhibited hepatic MTTP expression and dramatically reduced VLDL production, leading to severe hepatic steatosis and hypolipidemia. Pdia1-deletion did not affect mRNA expression or protein stability of MTTP but rather prevented Mttp mRNA translation. We demonstrate an essential role for PDIA1 in MTTP synthesis and function and show that PDIA1 interacts with APOB in an MTTP-independent manner via its molecular chaperone function to support APOB folding and secretion. CONCLUSIONS PDIA1 plays indispensable roles in APOB folding, MTTP synthesis and activity to support VLDL assembly. Thus, like APOB and MTTP, PDIA1 is an obligatory component of hepatic VLDL production.
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Affiliation(s)
- Zhouji Chen
- Degenerative Diseases Program, Center for Genetics and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd, La Jolla CA 92037, USA.
| | - Shiyu Wang
- Degenerative Diseases Program, Center for Genetics and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd, La Jolla CA 92037, USA
| | - Anita Pottekat
- Degenerative Diseases Program, Center for Genetics and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd, La Jolla CA 92037, USA
| | - Alec Duffey
- Degenerative Diseases Program, Center for Genetics and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd, La Jolla CA 92037, USA
| | - Insook Jang
- Degenerative Diseases Program, Center for Genetics and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd, La Jolla CA 92037, USA
| | - Benny H Chang
- Section of Nephrology, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaehyung Cho
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Brian N Finck
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicholas O Davidson
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Randal J Kaufman
- Degenerative Diseases Program, Center for Genetics and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd, La Jolla CA 92037, USA.
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18
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Luo Y, Gu Z, Liao W, Huang Y, Perez-Aguilar JM, Luo Y, Chen L. Villin headpiece unfolding upon binding to boridene mediated by the "anchoring-perturbation" mechanism. iScience 2024; 27:108577. [PMID: 38170080 PMCID: PMC10758975 DOI: 10.1016/j.isci.2023.108577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
We employ molecular dynamics (MD) simulations to investigate the influence of boridene on the behavior of a protein model, HP35, with the aim of assessing the potential biotoxicity of boridene. Our MD results reveal that HP35 can undergo unfolding via an "anchoring-perturbation" mechanism upon adsorption onto the boridene surface. Specifically, the third helix of HP35 becomes tightly anchored to the boridene surface through strong electrostatic interactions between the abundant molybdenum atoms on the boridene surface and the oxygen atoms on the HP35 backbone. Meanwhile, the first helix, experiencing continuous perturbation from the surrounding water solution over an extended period, suffers from potential breakage of hydrogen bonds, ultimately resulting in its unfolding. Our findings not only propose, for the first time to our knowledge, the "anchoring-perturbation" mechanism as a guiding principle for protein unfolding but also reveal the potential toxicity of boridene on protein structures.
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Affiliation(s)
- Yuqi Luo
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, No. 187, Guanlan Road, Longhua District, Shenzhen, Guangdong Province 518110, China
| | - Zonglin Gu
- College of Physical Science and Technology, Yangzhou University, Jiangsu 225009, China
| | - Weihua Liao
- Department of Radiology, Guangzhou Nansha District Maternal and Child Health Hospital, No. 103, Haibang Road, Nansha District, Guangzhou, Guangdong Province 511457, China
| | - Yiwen Huang
- Department of Emergency, Nansha Hospital, Guangzhou First People’s Hospital, Guangzhou, Guangdong, China
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - Yanbo Luo
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, No. 187, Guanlan Road, Longhua District, Shenzhen, Guangdong Province 518110, China
| | - Longzhen Chen
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, No. 187, Guanlan Road, Longhua District, Shenzhen, Guangdong Province 518110, China
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19
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Sun H, Le S, Guo Z, Chen H. Exploring the free energy landscape of proteins using magnetic tweezers. Methods Enzymol 2024; 694:237-261. [PMID: 38492953 DOI: 10.1016/bs.mie.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
Proteins fold to their native states by searching through the free energy landscapes. As single-domain proteins are the basic building block of multiple-domain proteins or protein complexes composed of subunits, the free energy landscapes of single-domain proteins are of critical importance to understand the folding and unfolding processes of proteins. To explore the free energy landscapes of proteins over large conformational space, the stability of native structure is perturbed by biochemical or mechanical means, and the conformational transition process is measured. In single molecular manipulation experiments, stretching force is applied to proteins, and the folding and unfolding transitions are recorded by the extension time course. Due to the broad force range and long-time stability of magnetic tweezers, the free energy landscape over large conformational space can be obtained. In this article, we describe the magnetic tweezers instrument design, protein construct design and preparation, fluid chamber preparation, common-used measuring protocols including force-ramp and force-jump measurements, and data analysis methods to construct the free energy landscape. Single-domain cold shock protein is introduced as an example to build its free energy landscape by magnetic tweezers measurements.
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Affiliation(s)
- Hao Sun
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China
| | - Shimin Le
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, P.R. China
| | - Zilong Guo
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China.
| | - Hu Chen
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China; Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, P.R. China.
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20
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Avellaneda MJ, Koers EJ, Sunderlikova V, Tans SJ. Protein Tethering for Single-Molecule Force Spectroscopy. Methods Mol Biol 2024; 2694:57-67. [PMID: 37823999 DOI: 10.1007/978-1-0716-3377-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Molecular manipulation by optical tweezers is a central technique to study the folded states of individual proteins and how they depend on interactions with molecules including DNA, ligands, and other proteins. One of the key challenges of this approach is to stably attach DNA handles in an efficient manner. Here, we provide detailed descriptions of a universal approach to covalently link long DNA tethers of up to 5000 base pairs to proteins with or without native cysteines.
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21
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Bonde B, Patil P, Choubey B. The Future of Drug Development with Quantum Computing. Methods Mol Biol 2024; 2716:153-179. [PMID: 37702939 DOI: 10.1007/978-1-0716-3449-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Novel medication development is a time-consuming and expensive multistage procedure. Recent technology developments have lowered timeframes, complexity, and cost dramatically. Current research projects are driven by AI and machine learning computational models. This chapter will introduce quantum computing (QC) to drug development issues and provide an in-depth discussion of how quantum computing may be used to solve various drug discovery problems. We will first discuss the fundamentals of QC, a review of known Hamiltonians, how to apply Hamiltonians to drug discovery challenges, and what the noisy intermediate-scale quantum (NISQ) era methods and their limitations are.We will further discuss how these NISQ era techniques can aid with specific drug discovery challenges, including protein folding, molecular docking, AI-/ML-based optimization, and novel modalities for small molecules and RNA secondary structures. Consequently, we will discuss the latest QC landscape's opportunities and challenges.
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Affiliation(s)
- Bhushan Bonde
- Evotec (UK) Ltd., Oxfordshire, UK.
- Digital Futures Institute, University of Suffolk, Ipswich, UK.
| | - Pratik Patil
- Evotec (UK) Ltd., Oxfordshire, UK
- Digital Futures Institute, University of Suffolk, Ipswich, UK
| | - Bhaskar Choubey
- Digital Futures Institute, University of Suffolk, Ipswich, UK
- Chair of Analogue Circuits and Image Sensors, Siegen University, Siegen, Germany
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22
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Pedrazzini E, Vitale A. Protein Biosynthesis and Maturation in the ER. Methods Mol Biol 2024; 2772:191-205. [PMID: 38411815 DOI: 10.1007/978-1-0716-3710-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The endoplasmic reticulum takes care of the folding, assembly, and quality control of thousands of proteins destined to the different compartments of the endomembrane system or to be secreted in the apoplast. Here we describe how these early events in the life of all these proteins can be followed biochemically by using velocity or isopycnic ultracentrifugation, metabolic labelling with radioactive amino acids, drug treatments, and immunoselection in various conditions and, in certain cases, predicted in silico by algorithms.
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Affiliation(s)
- Emanuela Pedrazzini
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Milan, Italy.
| | - Alessandro Vitale
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Milan, Italy
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23
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Coto ALDS, Pereira AA, Oliveira SD, Moritz MNDO, Franco da Rocha AM, Dores-Silva PR, da Silva NSM, de Araújo Nogueira AR, Gava LM, Seraphim TV, Borges JC. Structural characterization of the human DjC20/HscB cochaperone in solution. Biochim Biophys Acta Proteins Proteom 2024; 1872:140970. [PMID: 37871810 DOI: 10.1016/j.bbapap.2023.140970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/27/2023] [Accepted: 10/14/2023] [Indexed: 10/25/2023]
Abstract
J-domain proteins (JDPs) form a very large molecular chaperone family involved in proteostasis processes, such as protein folding, trafficking through membranes and degradation/disaggregation. JDPs are Hsp70 co-chaperones capable of stimulating ATPase activity as well as selecting and presenting client proteins to Hsp70. In mitochondria, human DjC20/HscB (a type III JDP that possesses only the conserved J-domain in some region of the protein) is involved in [FeS] protein biogenesis and assists human mitochondrial Hsp70 (HSPA9). Human DjC20 possesses a zinc-finger domain in its N-terminus, which closely contacts the J-domain and appears to be essential for its function. Here, we investigated the hDjC20 structure in solution as well as the importance of Zn+2 for its stability. The recombinant hDjC20 was pure, folded and capable of stimulating HSPA9 ATPase activity. It behaved as a slightly elongated monomer, as attested by small-angle X-ray scattering and SEC-MALS. The presence of Zn2+ in the hDjC20 samples was verified, a stoichiometry of 1:1 was observed, and its removal by high concentrations of EDTA and DTPA was unfeasible. However, thermal and chemical denaturation in the presence of EDTA led to a reduction in protein stability, suggesting a synergistic action between the chelating agent and denaturators that facilitate protein unfolding depending on metal removal. These data suggest that the affinity of Zn+2 for the protein is very high, evidencing its importance for the hDjC20 structure.
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Affiliation(s)
| | - Arthur Alexandre Pereira
- São Carlos Institute of Chemistry, University of São Paulo - USP, 13560-970 São Carlos, SP, Brazil
| | - Sabrina Dorta Oliveira
- São Carlos Institute of Chemistry, University of São Paulo - USP, 13560-970 São Carlos, SP, Brazil
| | | | | | | | | | | | | | - Thiago Vagas Seraphim
- São Carlos Institute of Chemistry, University of São Paulo - USP, 13560-970 São Carlos, SP, Brazil
| | - Júlio César Borges
- São Carlos Institute of Chemistry, University of São Paulo - USP, 13560-970 São Carlos, SP, Brazil.
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24
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Mora M, Tapia-Rojo R, Garcia-Manyes S. Unfolding and Refolding Proteins Using Single-Molecule AFM. Methods Mol Biol 2024; 2694:339-354. [PMID: 37824012 DOI: 10.1007/978-1-0716-3377-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Single-molecule atomic force microscopy (AFM) allows capturing the conformational dynamics of an individual molecule under force. In this chapter, we describe a protocol for conducting a protein nanomechanical experiment using AFM, covering both the force-extension and force-clamp modes. Combined, these experiments provide an integrated vista of the molecular mechanisms-and their associated kinetics-underpinning the mechanical unfolding and refolding of individual proteins when exposed to mechanical load.
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Affiliation(s)
- Marc Mora
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK
| | - Rafael Tapia-Rojo
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK
| | - Sergi Garcia-Manyes
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK.
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25
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Barbhuiya TK, Jayarathna DK, Gilmour R, Smet-Nocca C, Gandhi NS. Characterization of Posttranslationally Modified PHF-1 Tau Peptides Using Gaussian Accelerated Molecular Dynamics Simulation. Methods Mol Biol 2024; 2754:3-31. [PMID: 38512658 DOI: 10.1007/978-1-0716-3629-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
The microtubule-associated protein, Tau, is an intrinsically disordered protein that plays a crucial role in neurodegenerative diseases like Alzheimer's disease. The posttranslational modifications across the Tau protein domains are involved in regulating Tau protein's function and disease onset. Of the various posttranslational modifications at Ser, Thr, and Tyr sites, O-GlcNAcylation and phosphorylation are the most critical ones, playing a vital role in Tau aggregation and tauopathies. To understand the function, it is essential to characterize the structural changes associated with Tau modification. Previous experimental studies have focused on high-resolution nuclear magnetic resonance techniques to structurally characterize the effect of phosphorylation, O-GlcNAcylation, and combination of both PTMs on Tau conformation in small peptides centered on the PHF-1 epitope from amino acid 392 to 411. The structural characterization using atomistic molecular dynamics simulation of such disordered peptides requires long simulation time, proper sampling method, and utilization of appropriate force fields for accurate determination of conformational ensembles, resembling the experimental data. This chapter details the protocol for the structural characterization of modified Tau peptides using the CHARMM36m force field and enhanced sampling methods like Gaussian accelerated molecular dynamics (GaMD) simulation. We have focused on a detailed explanation of the GaMD method and analyses of molecular dynamics trajectories to explain the relationship between two modifications, phospho- and glyco-, at C-terminus of Tau protein and its stable conformation over the longer simulation timeframes. The analyses involve energetics reweighting, clustering of simulation trajectories, and characterization of secondary structure using circular dichroism data from the simulation. The reader can utilize this protocol to investigate the structures of complex proteins, especially the disordered ones.
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Affiliation(s)
- Tabassum Khair Barbhuiya
- School of Chemistry and Physics, Faculty of Science, Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
- Cancer and Ageing Research Program, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Dulari K Jayarathna
- School of Chemistry and Physics, Faculty of Science, Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Raechelle Gilmour
- School of Chemistry and Physics, Faculty of Science, Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Caroline Smet-Nocca
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Neha S Gandhi
- School of Chemistry and Physics, Faculty of Science, Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia.
- Cancer and Ageing Research Program, Translational Research Institute, Woolloongabba, QLD, Australia.
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Vance TDR. Ice Isn't the Only Crystal in Town: Structure Determination of Ice-Binding Proteins via X-Ray Crystallography. Methods Mol Biol 2024; 2730:35-62. [PMID: 37943449 DOI: 10.1007/978-1-0716-3503-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Ice-binding proteins (IBPs) are proteins that have the remarkable ability to bind to ice, and their study has intrigued researchers for decades. This chapter explores the importance of structural biology in understanding IBPs and highlights the significant contributions of IBPs to the field of structural biology. The structures of various IBPs from different organisms have been elucidated, revealing key elements involved in ice binding. Structural biology techniques, including nuclear magnetic resonance (NMR) spectroscopy, transmission electron cryo-microscopy (cryo-EM), and X-ray crystallography, play crucial roles in solving protein structures. This article focuses on X-ray crystallography as a tool for investigating IBP structures, providing insights into its theoretical and practical aspects, experimental workflows, and common pitfalls to avoid.
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Affiliation(s)
- Tyler D R Vance
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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27
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Das D, Ainavarapu SRK. Circular permutation at azurin's active site slows down its folding. J Biol Inorg Chem 2023; 28:737-749. [PMID: 37957357 DOI: 10.1007/s00775-023-02023-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Circular permutation (CP) is a technique by which the primary sequence of a protein is rearranged to create new termini. The connectivity of the protein is altered but the overall protein structure generally remains unperturbed. Understanding the effect of CP can help design robust proteins for numerous applications such as in genetic engineering, optoelectronics, and improving catalytic activity. Studies on different protein topologies showed that CP usually affects protein stability as well as unfolding rates. Though a significant number of proteins contain metals or other cofactors, reports of metalloprotein CPs are rare. Thus, we chose a bacterial metalloprotein, azurin, and its CP within the metal-binding site (cpF114). We studied the stabilities, folding, and unfolding rates of apo- and Zn2+-bound CP azurin using fluorescence and circular dichroism. The introduced CP had destabilizing effects on the protein. Also, the folding of the Zn2+-CP protein was much slower than that of the Zn2+-WT or apo-protein. We compared this study to our previously reported azurin-cpN42, where we had observed an equilibrium and kinetic intermediate. cpF114 exhibits an apparent two-state equilibrium unfolding but has an off-pathway kinetic intermediate. Our study hinted at CP as a method to modify the energy landscape of proteins to alter their folding pathways. WT azurin, being a faster folder, may have evolved to optimize the folding rate of metal-bound protein compared to its CPs, albeit all of them have the same structure and function. Our study underscores that protein sequence and protein termini positions are crucial for metalloproteins. TOC Figure. (Top) Zn2+-azurin WT structure (PDB code: 1E67) and 2-D topology diagram of Zn2+-cpF114 azurin. (Bottom) Cartoon diagram representing folding (red arrows) and unfolding (blue arrows) of apo- and Zn2+- WT and cpF114 azurins. The width of the arrows represents the rate of the corresponding processes.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai, 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai, 400005, India.
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28
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Dube A, Pullepu D, Kabir MA. Saccharomyces cerevisiae survival against heat stress entails a communication between CCT and cell wall integrity pathway. Biol Futur 2023; 74:519-527. [PMID: 37964139 DOI: 10.1007/s42977-023-00192-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/23/2023] [Indexed: 11/16/2023]
Abstract
The chaperonin TRiC/CCT is cytosolic cylindrical complex of 16 subunits encoded by eight essential genes CCT1-8. It contributes to folding 10% of cellular polypeptides in yeast. The strain carrying substitution point mutation G412E in the equatorial domain of Cct7p resulted in the improper folding of substrates. In this study, the Cct7p mutant exhibited sensitivity to non-optimal growth temperatures and cell wall stressors. Heat shock is known to disrupt cell wall and protein stability in budding yeast. Mitogen-activated protein kinase-mediated cell wall integrity pathway gets activated to compensate the perturbed cell wall. Overexpression of the PKC1 and SLT2 genes of MAPK signaling pathway in mutant rescued the growth and cell division defects. Additionally, the genes of the CWI pathway such as SED1, GFA1, PIR1, and RIM21 are down-regulated. The Cct7p mutant strain (G412E) is unable to withstand the heat stress due to the underlying defects in protein folding and cell wall maintenance. Taken together, our results strongly indicate the interaction between CCT and cell wall integrity pathway.
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Affiliation(s)
- Ankita Dube
- Department of Biochemistry, Indian Institute of Sciences, Bangalore, India
| | - Dileep Pullepu
- Molecular Biology and Genetics Unit, Molecular Mycology Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - M Anaul Kabir
- Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Calicut, Kerala, 673601, India.
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29
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Roterman I, Stapor K, Konieczny L. Role of environmental specificity in CASP results. BMC Bioinformatics 2023; 24:425. [PMID: 37950210 PMCID: PMC10638730 DOI: 10.1186/s12859-023-05559-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Recently, significant progress has been made in the field of protein structure prediction by the application of artificial intelligence techniques, as shown by the results of the CASP13 and CASP14 (Critical Assessment of Structure Prediction) competition. However, the question of the mechanism behind the protein folding process itself remains unanswered. Correctly predicting the structure also does not solve the problem of, for example, amyloid proteins, where a polypeptide chain with an unaltered sequence adopts a different 3D structure. RESULTS This work was an attempt at explaining the structural variation by considering the contribution of the environment to protein structuring. The application of the fuzzy oil drop (FOD) model to assess the validity of the selected models provided in the CASP13, CASP14 and CASP15 projects reveals the need for an environmental factor to determine the 3D structure of proteins. Consideration of the external force field in the form of polar water (Fuzzy Oil Drop) and a version modified by the presence of the hydrophobic compounds, FOD-M (FOD-Modified) reveals that the protein folding process is environmentally dependent. An analysis of selected models from the CASP competitions indicates the need for structure prediction as dependent on the consideration of the protein folding environment. CONCLUSIONS The conditions governed by the environment direct the protein folding process occurring in a certain environment. Therefore, the variation of the external force field should be taken into account in the models used in protein structure prediction.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Medyczna 7, 30-688, Krakow, Poland.
| | - Katarzyna Stapor
- Faculty of Automatic, Electronics and Computer Science, Department of Applied, Informatics, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland
| | - Leszek Konieczny
- Jagiellonian University - Medical College, Kopernika 7, 31-034, Krakow, Poland
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30
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Ecroyd H, Bartelt-Kirbach B, Ben-Zvi A, Bonavita R, Bushman Y, Casarotto E, Cecconi C, Lau WCY, Hibshman JD, Joosten J, Kimonis V, Klevit R, Liberek K, McMenimen KA, Miwa T, Mogk A, Montepietra D, Peters C, Rocchetti MT, Saman D, Sisto A, Secco V, Strauch A, Taguchi H, Tanguay M, Tedesco B, Toth ME, Wang Z, Benesch JLP, Carra S. The beauty and complexity of the small heat shock proteins: a report on the proceedings of the fourth workshop on small heat shock proteins. Cell Stress Chaperones 2023; 28:621-629. [PMID: 37462824 PMCID: PMC10746627 DOI: 10.1007/s12192-023-01360-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2023] [Indexed: 12/23/2023] Open
Abstract
The Fourth Cell Stress Society International workshop on small heat shock proteins (sHSPs), a follow-up to successful workshops held in 2014, 2016 and 2018, took place as a virtual meeting on the 17-18 November 2022. The meeting was designed to provide an opportunity for those working on sHSPs to reconnect and discuss their latest work. The diversity of research in the sHSP field is reflected in the breadth of topics covered in the talks presented at this meeting. Here we summarise the presentations at this meeting and provide some perspectives on exciting future topics to be addressed in the field.
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Affiliation(s)
- Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
| | | | - Anat Ben-Zvi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Raffaella Bonavita
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131, Naples, Italy
| | - Yevheniia Bushman
- Center for Protein Assemblies and Department Chemie, Technische Universität München, München, Germany
| | - Elena Casarotto
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti" (DiSFeB), Dipartimento di Eccellenza, Università degli Studi di Milano, Milan, Italy
| | - Ciro Cecconi
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena, Italy
- Istituto Nanoscienze-CNR-NANO, Center S3, Modena, Italy
| | - Wilson Chun Yu Lau
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - Jonathan D Hibshman
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joep Joosten
- Department of Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Virginia Kimonis
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California - Irvine, Orange, CA, 92868, USA
- Department of Neurology and Department of Pathology, University of California, Irvine, CA, 92697, USA
| | - Rachel Klevit
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Krzysztof Liberek
- Intercollegiate Faculty of Biotechnology, University of Gdansk, Gdansk, Poland
| | - Kathryn A McMenimen
- Program in Biochemistry and Department of Chemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
| | - Tsukumi Miwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8503, Japan
| | - Axel Mogk
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld, 282, Heidelberg, Germany
| | - Daniele Montepietra
- Istituto Nanoscienze-CNR-NANO, Center S3, Modena, Italy
- Department of Department of Chemical, Life and Environmental sustainability sciences, University of Parma, Parma, Italy
| | - Carsten Peters
- Center for Protein Assemblies and Department Chemie, Technische Universität München, München, Germany
| | - Maria Teresa Rocchetti
- Department of Clinical and Experimental Medicine, University of Foggia, 71122, Foggio, Italy
| | - Dominik Saman
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Angela Sisto
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences and Institute Born Bunge, University of Antwerp, Antwerpen, Belgium
| | - Valentina Secco
- Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Annika Strauch
- Center for Protein Assemblies and Department Chemie, Technische Universität München, München, Germany
| | - Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8503, Japan
| | - Morgan Tanguay
- Program in Biochemistry and Department of Chemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
| | - Barbara Tedesco
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti" (DiSFeB), Dipartimento di Eccellenza, Università degli Studi di Milano, Milan, Italy
| | - Melinda E Toth
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Temesvári krt. 62, Szeged, H-6726, Hungary
| | - Zihao Wang
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Justin L P Benesch
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Serena Carra
- Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy.
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31
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Wysocki R, Rodrigues JI, Litwin I, Tamás MJ. Mechanisms of genotoxicity and proteotoxicity induced by the metalloids arsenic and antimony. Cell Mol Life Sci 2023; 80:342. [PMID: 37904059 PMCID: PMC10616229 DOI: 10.1007/s00018-023-04992-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/12/2023] [Accepted: 09/29/2023] [Indexed: 11/01/2023]
Abstract
Arsenic and antimony are metalloids with profound effects on biological systems and human health. Both elements are toxic to cells and organisms, and exposure is associated with several pathological conditions including cancer and neurodegenerative disorders. At the same time, arsenic- and antimony-containing compounds are used in the treatment of multiple diseases. Although these metalloids can both cause and cure disease, their modes of molecular action are incompletely understood. The past decades have seen major advances in our understanding of arsenic and antimony toxicity, emphasizing genotoxicity and proteotoxicity as key contributors to pathogenesis. In this review, we highlight mechanisms by which arsenic and antimony cause toxicity, focusing on their genotoxic and proteotoxic effects. The mechanisms used by cells to maintain proteostasis during metalloid exposure are also described. Furthermore, we address how metalloid-induced proteotoxicity may promote neurodegenerative disease and how genotoxicity and proteotoxicity may be interrelated and together contribute to proteinopathies. A deeper understanding of cellular toxicity and response mechanisms and their links to pathogenesis may promote the development of strategies for both disease prevention and treatment.
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Affiliation(s)
- Robert Wysocki
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328, Wroclaw, Poland.
| | - Joana I Rodrigues
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30, Göteborg, Sweden
| | - Ireneusz Litwin
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328, Wroclaw, Poland
| | - Markus J Tamás
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30, Göteborg, Sweden.
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32
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de Paz-Lugo P, Lupiáñez JA, Sicilia J, Meléndez-Hevia E. Control analysis of collagen synthesis by glycine, proline and lysine in bovine chondrocytes in vitro - Its relevance for medicine and nutrition. Biosystems 2023; 232:105004. [PMID: 37598999 DOI: 10.1016/j.biosystems.2023.105004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
Collagen synthesis is severely diminished in osteoarthritis; thus, enhancing it may help the regeneration of cartilage. Collagen synthesis is submitted to a large procollagen cycle where the greater part of the newly synthesized protein is degraded inside the cell producing a huge waste of material and energy. We have applied the Metabolic Control Analysis approach to study the control of collagen synthesis flux by means of the response coefficients of the flux with respect to glycine, proline and lysine. Our results show that the main cause of the procollagen cycle is a protein misfolding mainly due to glycine scarcity, as well as a moderate deficiency of proline and lysine for collagen synthesis. Thus, increasing these amino acids in the diet (especially glycine) may well be a strategy for helping cartilage regeneration by enhancing collagen synthesis and reducing its huge waste in the procollagen cycle; this possibly contributes to the treatment and prevention of osteoarthritis.
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Affiliation(s)
- Patricia de Paz-Lugo
- Instituto del Metabolismo Celular, Calle Manuel de Falla nº15, La Laguna, 38208, Tenerife, Canary Islands, Spain.
| | - José Antonio Lupiáñez
- Universidad de Granada, Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias, Avda. Fuentenueva nº 1, 18071, Granada, Spain.
| | - Joaquín Sicilia
- Universidad de La Laguna, Departamento de Matemáticas, Estadística e Investigación Operativa, Avda. Astrofísico Francisco Sánchez, S/n. La Laguna, 38206, Tenerife, Canary Islands, Spain.
| | - Enrique Meléndez-Hevia
- Instituto del Metabolismo Celular, Calle Manuel de Falla nº15, La Laguna, 38208, Tenerife, Canary Islands, Spain.
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33
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Huang B, Kong L, Wang C, Ju F, Zhang Q, Zhu J, Gong T, Zhang H, Yu C, Zheng WM, Bu D. Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms. Genomics Proteomics Bioinformatics 2023; 21:913-925. [PMID: 37001856 PMCID: PMC10928435 DOI: 10.1016/j.gpb.2022.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 03/31/2023]
Abstract
Protein structure prediction is an interdisciplinary research topic that has attracted researchers from multiple fields, including biochemistry, medicine, physics, mathematics, and computer science. These researchers adopt various research paradigms to attack the same structure prediction problem: biochemists and physicists attempt to reveal the principles governing protein folding; mathematicians, especially statisticians, usually start from assuming a probability distribution of protein structures given a target sequence and then find the most likely structure, while computer scientists formulate protein structure prediction as an optimization problem - finding the structural conformation with the lowest energy or minimizing the difference between predicted structure and native structure. These research paradigms fall into the two statistical modeling cultures proposed by Leo Breiman, namely, data modeling and algorithmic modeling. Recently, we have also witnessed the great success of deep learning in protein structure prediction. In this review, we present a survey of the efforts for protein structure prediction. We compare the research paradigms adopted by researchers from different fields, with an emphasis on the shift of research paradigms in the era of deep learning. In short, the algorithmic modeling techniques, especially deep neural networks, have considerably improved the accuracy of protein structure prediction; however, theories interpreting the neural networks and knowledge on protein folding are still highly desired.
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Affiliation(s)
- Bin Huang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lupeng Kong
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; Changping Laboratory, Beijing 102206, China
| | - Chao Wang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Fusong Ju
- Microsoft Research AI4Science, Beijing 100080, China
| | - Qi Zhang
- Huawei Noah's Ark Lab, Wuhan 430206, China
| | - Jianwei Zhu
- Microsoft Research AI4Science, Beijing 100080, China
| | - Tiansu Gong
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haicang Zhang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhongke Big Data Academy, Zhengzhou 450046, China.
| | - Chungong Yu
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhongke Big Data Academy, Zhengzhou 450046, China.
| | - Wei-Mou Zheng
- Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Dongbo Bu
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhongke Big Data Academy, Zhengzhou 450046, China.
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Ciesielski SJ, Young C, Ciesielska EJ, Ciesielski GL. The Hsp70 and JDP proteins: Structure-function perspective on molecular chaperone activity. Enzymes 2023; 54:221-245. [PMID: 37945173 DOI: 10.1016/bs.enz.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Proteins are the most structurally diverse cellular biomolecules that act as molecular machines driving essential activities of all living organisms. To be functional, most of the proteins need to fold into a specific three-dimensional structure, which on one hand should be stable enough to oppose disruptive conditions and on the other hand flexible enough to allow conformational dynamics necessary for their biological functions. This compromise between stability and dynamics makes proteins susceptible to stress-induced misfolding and aggregation. Moreover, the folding process itself is intrinsically prone to conformational errors. Molecular chaperones are proteins that mitigate folding defects and maintain the structural integrity of the cellular proteome. Promiscuous Hsp70 chaperones are central to these processes and their activity depends on the interaction with obligatory J-domain protein (JDP) partners. In this review, we discuss structural aspects of Hsp70s, JDPs, and their interaction in the context of biological activities.
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Affiliation(s)
- Szymon J Ciesielski
- Department of Chemistry and Biochemistry, University of North Florida, Jacksonville, FL, United States.
| | - Cameron Young
- Department of Chemistry and Biochemistry, University of North Florida, Jacksonville, FL, United States
| | - Elena J Ciesielska
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL, United States; Department of Biology, University of North Florida, Jacksonville, FL, United States
| | - Grzegorz L Ciesielski
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL, United States; Department of Biology, University of North Florida, Jacksonville, FL, United States
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35
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Retamal-Farfán I, González-Higueras J, Galaz-Davison P, Rivera M, Ramírez-Sarmiento CA. Exploring the structural acrobatics of fold-switching proteins using simplified structure-based models. Biophys Rev 2023; 15:787-799. [PMID: 37681096 PMCID: PMC10480104 DOI: 10.1007/s12551-023-01087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/22/2023] [Indexed: 09/09/2023] Open
Abstract
Metamorphic proteins are a paradigm of the protein folding process, by encoding two or more native states, highly dissimilar in terms of their secondary, tertiary, and even quaternary structure, on a single amino acid sequence. Moreover, these proteins structurally interconvert between these native states in a reversible manner at biologically relevant timescales as a result of different environmental cues. The large-scale rearrangements experienced by these proteins, and their sometimes high mass interacting partners that trigger their metamorphosis, makes the computational and experimental study of their structural interconversion challenging. Here, we present our efforts in studying the refolding landscapes of two quintessential metamorphic proteins, RfaH and KaiB, using simplified dual-basin structure-based models (SBMs), rigorously footed on the energy landscape theory of protein folding and the principle of minimal frustration. By using coarse-grained models in which the native contacts and bonded interactions extracted from the available experimental structures of the two native states of RfaH and KaiB are merged into a single Hamiltonian, dual-basin SBM models can be generated and savvily calibrated to explore their fold-switch in a reversible manner in molecular dynamics simulations. We also describe how some of the insights offered by these simulations have driven the design of experiments and the validation of the conformational ensembles and refolding routes observed using this simple and computationally efficient models.
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Affiliation(s)
- Ignacio Retamal-Farfán
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Jorge González-Higueras
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- Department of Chemistry, Faculty of Science, McGill University, Montreal, Quebec H3A 0B8 Canada
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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Abstract
A comparative analysis between two problems-apparently unrelated-which are solved in a period of ~400 years, viz., the accurate prediction of both the planetary orbits and the protein structures, leads to inferred conjectures that go far beyond the existence of a common path in their resolution, i.e., observation → pattern recognition → modeling. The preliminary results from this analysis indicate that complementary science, together with a new perspective on protein folding, may help us discover common features that could contribute to a more in-depth understanding of still-unsolved problems such as protein folding.
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Affiliation(s)
- Jorge A. Vila
- IMASL-CONICET, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700 San Luis, Argentina
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Abstract
Over the past decade, myriads of studies have highlighted the central role of protein condensation in subcellular compartmentalization and spatiotemporal organization of biological processes. Conceptually, protein condensation stands at the highest level in protein structure hierarchy, accounting for the assembly of bodies ranging from thousands to billions of molecules and for densities ranging from dense liquids to solid materials. In size, protein condensates range from nanocondensates of hundreds of nanometers (mesoscopic clusters) to phase-separated micron-sized condensates. In this review, we focus on protein nanocondensation, a process that can occur in subsaturated solutions and can nucleate dense liquid phases, crystals, amorphous aggregates, and fibers. We discuss the nanocondensation of proteins in the light of general physical principles and examine the biophysical properties of several outstanding examples of nanocondensation. We conclude that protein nanocondensation cannot be fully explained by the conceptual framework of micron-scale biomolecular condensation. The evolution of nanocondensates through changes in density and order is currently under intense investigation, and this should lead to the development of a general theoretical framework, capable of encompassing the full range of sizes and densities found in protein condensates.
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Affiliation(s)
- Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
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Grigorjew A, Gynter A, Dias FHC, Buchfink B, Drost HG, Tomescu AI. Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD. Genome Biol 2023; 24:168. [PMID: 37461051 DOI: 10.1186/s13059-023-03008-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023] Open
Abstract
Sequence alignments are the foundations of life science research, but most innovation so far focuses on optimal alignments, while information derived from suboptimal solutions is ignored. We argue that one optimal alignment per pairwise sequence comparison is a reasonable approximation when dealing with very similar sequences but is insufficient when exploring the biodiversity of the protein universe at tree-of-life scale. To overcome this limitation, we introduce pairwise alignment-safety to uncover the amino acid positions robustly shared across all suboptimal solutions. We implement EMERALD, a software library for alignment-safety inference, and apply it to 400k sequences from the SwissProt database.
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Affiliation(s)
- Andreas Grigorjew
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Artur Gynter
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Fernando H C Dias
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Benjamin Buchfink
- Computational Biology Group, Max Planck Institute for Biology, Tübingen, Germany
| | - Hajk-Georg Drost
- Computational Biology Group, Max Planck Institute for Biology, Tübingen, Germany.
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Richards BJ, Slavin M, Oliveira AN, Sanfrancesco VC, Hood DA. Mitochondrial protein import and UPR(mt) in skeletal muscle remodeling and adaptation. Semin Cell Dev Biol 2023; 143:28-36. [PMID: 35063351 DOI: 10.1016/j.semcdb.2022.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/20/2021] [Accepted: 01/04/2022] [Indexed: 01/03/2023]
Abstract
The biogenesis of mitochondria requires the coordinated expression of the nuclear and the mitochondrial genomes. However, the vast majority of gene products within the organelle are encoded in the nucleus, synthesized in the cytosol, and imported into mitochondria via the protein import machinery, which permit the entry of proteins to expand the mitochondrial network. Once inside, proteins undergo a maturation and folding process brought about by enzymes comprising the unfolded protein response (UPRmt). Protein import and UPRmt activity must be synchronized and matched with mtDNA-encoded subunit synthesis for proper assembly of electron transport chain complexes to avoid proteotoxicity. This review discusses the functions of the import and UPRmt systems in mammalian skeletal muscle, as well as how exercise alters the equilibrium of these pathways in a time-dependent manner, leading to a new steady state of mitochondrial content resulting in enhanced oxidative capacity and improved muscle health.
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Zhang Q, Feng R, Miao R, Lin J, Cao L, Ni Y, Li W, Zhao X. Combined transcriptomics and metabolomics analysis reveals the molecular mechanism of heat tolerance of Le023M, a mutant in Lentinulaedodes. Heliyon 2023; 9:e18360. [PMID: 37519752 PMCID: PMC10372740 DOI: 10.1016/j.heliyon.2023.e18360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023] Open
Abstract
Lentinula edodes, one of the most highly regarded edible mushrooms in China, is susceptible to damage from high temperatures. However, a mutant strain derived from L. edodes, known as Le023M, has shown exceptional thermotolerance. Compared to the original strain Le023, Le023M exhibited accelerated mycelial recovery following heat stress. Through RNA-seq analysis, the majority of differentially expressed genes (DEGs) were found to be associated with functions such as "protein refolding", "protein unfolding", "protein folding", and "response to heat", all of which are closely linked to heat shock proteins. Furthermore, qRT-PCR results revealed significant accumulation of heat shock-related genes in Le023M under heat stress. GC-MS analysis indicated elevated levels of trehalose, aspartate, and glutamate in Le023M when subjected to heat stress. The highly expressed genes involved in these metabolic pathways were predominantly found in Le023M. Collectively, these findings highlight the following: (i) the crucial role of heat shock proteins (HSPs) in the thermo-resistant mechanisms of Le023M; (ii) the potential of trehalose accumulation in Le023M to enhance mycelium resistance to heat stress; and (iii) the induction of aspartate and glutamate accumulation in response to heat stress. These results shed light on the molecular mechanisms underlying the thermotolerance of Le023M, providing valuable insights for further understanding and improving heat stress response in L. edodes. The findings also highlight the potential applications of Le023M in the cultivation and production of L. edodes under high-temperature conditions.
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Affiliation(s)
- Qin Zhang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China
- Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China
| | - Rencai Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China
- Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China
| | - Renyun Miao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China
- Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China
| | - Junbin Lin
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China
- Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China
| | - Luping Cao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Yanqing Ni
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China
| | - Wensheng Li
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China
| | - Xu Zhao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China
- Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China
- Facility Agriculture and Equipment Research Institute, Gansu Academy of Agri-engineering Technology, Wuwei, 733006, Gansu, China
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Bhatti JS, Kaur S, Mishra J, Dibbanti H, Singh A, Reddy AP, Bhatti GK, Reddy PH. Targeting dynamin-related protein-1 as a potential therapeutic approach for mitochondrial dysfunction in Alzheimer's disease. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166798. [PMID: 37392948 DOI: 10.1016/j.bbadis.2023.166798] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease that manifests its pathology through synaptic damage, mitochondrial abnormalities, microRNA deregulation, hormonal imbalance, increased astrocytes & microglia, accumulation of amyloid β (Aβ) and phosphorylated Tau in the brains of AD patients. Despite extensive research, the effective treatment of AD is still unknown. Tau hyperphosphorylation and mitochondrial abnormalities are involved in the loss of synapses, defective axonal transport and cognitive decline in patients with AD. Mitochondrial dysfunction is evidenced by enhanced mitochondrial fragmentation, impaired mitochondrial dynamics, mitochondrial biogenesis and defective mitophagy in AD. Hence, targeting mitochondrial proteins might be a promising therapeutic strategy in treating AD. Recently, dynamin-related protein 1 (Drp1), a mitochondrial fission protein, has gained attention due to its interactions with Aβ and hyperphosphorylated Tau, altering mitochondrial morphology, dynamics, and bioenergetics. These interactions affect ATP production in mitochondria. A reduction in Drp1 GTPase activity protects against neurodegeneration in AD models. This article provides a comprehensive overview of Drp1's involvement in oxidative damage, apoptosis, mitophagy, and axonal transport of mitochondria. We also highlighted the interaction of Drp1 with Aβ and Tau, which may contribute to AD progression. In conclusion, targeting Drp1 could be a potential therapeutic approach for preventing AD pathology.
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Affiliation(s)
- Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India.
| | - Satinder Kaur
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
| | - Jayapriya Mishra
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
| | | | - Arti Singh
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
| | - Arubala P Reddy
- Nutritional Sciences Department, College of Human Sciences, Texas Tech University, 1301 Akron Ave, Lubbock, TX 79409, USA.
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India.
| | - P Hemachandra Reddy
- Nutritional Sciences Department, College of Human Sciences, Texas Tech University, 1301 Akron Ave, Lubbock, TX 79409, USA; Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Public Health, Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Speech, Language, and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
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42
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Puri S, Liu CY, Hu IC, Lai CH, Hsu STD, Lyu PC. Elucidation of the folding pathway of a circular permutant of topologically knotted YbeA by tryptophan substitutions. Biochem Biophys Res Commun 2023; 672:81-88. [PMID: 37343318 DOI: 10.1016/j.bbrc.2023.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023]
Abstract
CP74 is an engineered circular permutant of a deep trefoil knotted SpoU-TrmD (SPOUT) RNA methyl transferase protein YbeA from E. coli. We have previously established that the circular permutation unties the knotted topology of YbeA and CP74 forms a domain-swapped dimer with a large dimeric interface of ca. 4600 Å2. To understand the impact of domain-swapping and the newly formed hinge region joining the two folded domains on the folding and stability of CP74, the five equally spaced tryptophan residues were individually substituted into phenylalanine to monitor their conformational and stability changes by a battery of biophysical tools. Far-UV circular dichroism, intrinsic fluorescence, and small-angle X-ray scattering dictated minimal global conformational perturbations to the native structures in the tryptophan variants. The structures of the tryptophan variants also showed the conservation of the domain-swapped ternary structure with the exception that the W72F exhibited significant asymmetry in the α-helix 5. Comparative global thermal and chemical stability analyses indicated the pivotal role of W100 in the folding of CP74 followed by W19 and W72. Solution-state NMR spectroscopy and hydrogen-deuterium exchange mass spectrometry further revealed the accumulation of a native-like intermediate state in which the hinge region made important contributions to maintain the domain-swapped ternary structure of CP74.
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Affiliation(s)
- Sarita Puri
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Yu Liu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - I-Chen Hu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Chih-Hsuan Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan; Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashihiroshima, 739-8527, Japan.
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
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43
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Xiao N, Ma H, Gao H, Yang J, Tong D, Gan D, Yang J, Li C, Liu K, Li Y, Chen Z, Yin C, Li X, Wang H. Structure-function crosstalk in liver cancer research: Protein structuromics. Int J Biol Macromol 2023:125291. [PMID: 37315670 DOI: 10.1016/j.ijbiomac.2023.125291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/04/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023]
Abstract
Liver cancer can be primary (starting in the liver) or secondary (cancer that has spread from elsewhere to the liver, known as liver metastasis). Liver metastasis is more common than primary liver cancer. Despite great advances in molecular biology methods and treatments, liver cancer is still associated with a poor survival rate and a high death rate, and there is no cure. Many questions remain regarding the mechanisms of liver cancer occurrence and development as well as tumor reoccurrence after treatment. In this study, we assessed the protein structural features of 20 oncogenes and 20 anti-oncogenes via protein structure and dynamic analysis methods and 3D structural and systematic analyses of the structure-function relationships of proteins. Our aim was to provide new insights that may inform research on the development and treatment of liver cancer.
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Affiliation(s)
- Nan Xiao
- Department of Medical Science, Medical College of Jinzhou Medical University, Jinzhou City, Liaoning Province, China.
| | - Hongming Ma
- Department of Oncology, China Emergency General Hospital City, Beijing, China
| | - Hong Gao
- Department of Oncology, China Emergency General Hospital City, Beijing, China
| | - Jing Yang
- Department of Computer Center, Medical College of Jinzhou Medical University, Jinzhou City, Liaoning Province, China
| | - Dan Tong
- Department of Nurse, Medical College of Jinzhou Medical University, Jinzhou City, Liaoning Province, China
| | - Dingzhu Gan
- Department of Publicity, Peking Union Medical College, Beijing, China
| | - Jinhua Yang
- Department of Development and Production, Institute of Medical Biology, Peking Union Medical College, Kunming City, Yunnan Province, China
| | - Chi Li
- Department of Anesthesiology, Medical College of Jinzhou Medical University, Jinzhou City, Liaoning Province, China
| | - Kang Liu
- Department of Medical Science, Medical College of Jinzhou Medical University, Jinzhou City, Liaoning Province, China
| | - Yingxin Li
- Department of Medical Science, Medical College of Jinzhou Medical University, Jinzhou City, Liaoning Province, China
| | - Zhibo Chen
- Department of Medical Science, Medical College of Jinzhou Medical University, Jinzhou City, Liaoning Province, China
| | - Chaoqun Yin
- Department of Medical Science, Medical College of Jinzhou Medical University, Jinzhou City, Liaoning Province, China
| | - Xingqi Li
- Department of Medicine, Medical College of Jinzhou Medical University, Jinzhou City, Liaoning Province, China
| | - Hongwu Wang
- Department of Respiratory and Critical Care Medicine, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, China
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44
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Serebryany E, Zhao VY, Park K, Bitran A, Trauger SA, Budnik B, Shakhnovich EI. Systematic conformation-to-phenotype mapping via limited deep sequencing of proteins. Mol Cell 2023; 83:1936-1952.e7. [PMID: 37267908 DOI: 10.1016/j.molcel.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 01/29/2023] [Accepted: 05/03/2023] [Indexed: 06/04/2023]
Abstract
Non-native conformations drive protein-misfolding diseases, complicate bioengineering efforts, and fuel molecular evolution. No current experimental technique is well suited for elucidating them and their phenotypic effects. Especially intractable are the transient conformations populated by intrinsically disordered proteins. We describe an approach to systematically discover, stabilize, and purify native and non-native conformations, generated in vitro or in vivo, and directly link conformations to molecular, organismal, or evolutionary phenotypes. This approach involves high-throughput disulfide scanning (HTDS) of the entire protein. To reveal which disulfides trap which chromatographically resolvable conformers, we devised a deep-sequencing method for double-Cys variant libraries of proteins that precisely and simultaneously locates both Cys residues within each polypeptide. HTDS of the abundant E. coli periplasmic chaperone HdeA revealed distinct classes of disordered hydrophobic conformers with variable cytotoxicity depending on where the backbone was cross-linked. HTDS can bridge conformational and phenotypic landscapes for many proteins that function in disulfide-permissive environments.
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Affiliation(s)
- Eugene Serebryany
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Victor Y Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kibum Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amir Bitran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sunia A Trauger
- Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Bogdan Budnik
- Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
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45
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Atang AE, Rebbeck RT, Thomas DD, Avery AW. Cardiomyopathy-associated variants alter the structure and function of the α-actinin-2 actin-binding domain. Biochem Biophys Res Commun 2023; 670:12-18. [PMID: 37271035 DOI: 10.1016/j.bbrc.2023.05.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023]
Abstract
Hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), and restrictive cardiomyopathy (RCM) are characterized by thickening, thinning, or stiffening, respectively, of the ventricular myocardium, resulting in diastolic or systolic dysfunction that can lead to heart failure and sudden cardiac death. Recently, variants in the ACTN2 gene, encoding the protein α-actinin-2, have been reported in HCM, DCM, and RCM patients. However, functional data supporting the pathogenicity of these variants is limited, and potential mechanisms by which these variants cause disease are largely unexplored. Currently, NIH ClinVar lists 34 ACTN2 missense variants, identified in cardiomyopathy patients, which we predict are likely to disrupt actin binding, based on their localization to specific substructures in the α-actinin-2 actin binding domain (ABD). We investigated the molecular consequences of three ABD localized, HCM-associated variants: A119T, M228T and T247 M. Using circular dichroism, we demonstrate that the mutant ABD proteins can attain a well-folded state. However, thermal denaturation studies show that all three mutations are destabilizing, suggesting a structural disruption. Importantly, A119T decreased actin binding, and M228T and T247M cause increased actin binding. We suggest that altered actin binding underlies pathogenesis for cardiomyopathy mutations localizing to the ABD of α-actinin-2.
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Affiliation(s)
- Alexandra E Atang
- Department of Chemistry, Oakland University, Rochester, MI, 48309-4479, USA
| | - Robyn T Rebbeck
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, 55455, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, 55455, USA
| | - Adam W Avery
- Department of Chemistry, Oakland University, Rochester, MI, 48309-4479, USA.
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Thewasano N, Germany EM, Maruno Y, Nakajima Y, Shiota T. Categorization of Escherichia coli Outer Membrane Proteins by Dependence on Accessory Proteins of the β-barrel Assembly Machinery Complex. J Biol Chem 2023:104821. [PMID: 37196764 PMCID: PMC10300371 DOI: 10.1016/j.jbc.2023.104821] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/20/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is populated by various outer membrane proteins (OMPs) that fold into a unique β-barrel transmembrane domain. Most OMPs are assembled into the OM by the β-barrel assembly machinery (BAM) complex. In Escherichia coli, the BAM complex is composed of two essential proteins (BamA and BamD) and three non-essential accessory proteins (BamB, BamC, and BamE). The currently proposed molecular mechanisms of the BAM complex involve only essential subunits, with the function of the accessory proteins remaining largely unknown. Here, we compared the accessory protein requirements for the assembly of seven different OMPs, 8- to 22-stranded, by our in vitro reconstitution assay using an E. coli mid-density membrane (EMM). BamE was responsible for the full efficiency of the assembly of all tested OMPs, as it enhanced the stability of essential subunit binding. BamB increased the assembly efficiency of more than 16-stranded OMPs, whereas BamC was not required for the assembly of any tested OMPs. Our categorization of the requirements of BAM complex accessory proteins in the assembly of substrate OMPs enables us to identify potential targets for the development of new antibiotics.
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Affiliation(s)
- Nakajohn Thewasano
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Edward M Germany
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yuki Maruno
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yukari Nakajima
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Takuya Shiota
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
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Vila JA. Rethinking the protein folding problem from a new perspective. Eur Biophys J 2023:10.1007/s00249-023-01657-w. [PMID: 37165178 DOI: 10.1007/s00249-023-01657-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/16/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023]
Abstract
One of the main concerns of Anfinsen was to reveal the connection between the amino-acid sequence and their biologically active conformation. This search gave rise to two crucial questions in structural biology, namely, why the proteins fold and how a sequence encodes its folding. As to the why, he proposes a plausible answer, namely, the thermodynamic hypothesis. As to the how, this remains an unsolved challenge. Consequently, the protein folding problem is examined here from a new perspective, namely, as an 'analytic whole'. Conceiving the protein folding in this way enabled us to (i) examine in detail why the force-field-based approaches have failed, among other purposes, in their ability to predict the three-dimensional structure of a protein accurately; (ii) propose how to redefine them to prevent these shortcomings, and (iii) conjecture on the origin of the state-of-the-art numerical-methods success to predict the tridimensional structure of proteins accurately.
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Affiliation(s)
- Jorge A Vila
- IMASL-CONICET, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina.
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48
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Lewis A, Pham T, Nguyen N, Graf A, Cheng KH. Lipid domain boundary triggers membrane damage and protein folding of human islet amyloid polypeptide in the early pathogenesis of amyloid diseases. Biophys Chem 2023; 296:106993. [PMID: 36898349 DOI: 10.1016/j.bpc.2023.106993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
The misfolding and self-aggregation of human Islet Amyloid Polypeptide (hIAPP) are linked to the onset of type 2 diabetes (T2D). However, the mechanism of how the disordered hIAPP aggregates trigger membrane damage leading to the loss of Islet cells in T2D is unknown. Using coarse-grained (CG) and all-atom (AA) molecular dynamics simulations, we have investigated the membrane-disruption behaviors of hIAPP oligomers on the phase-separated lipid nanodomains that mimic the highly heterogeneous lipid raft structures of cell membranes. Our results revealed that hIAPP oligomers preferentially bind to the liquid-ordered and liquid-disordered domain boundary around two hydrophobic residues at L16 and I26, and lipid acyl chain order disruption and beta-sheet formation occur upon hIAPP binding to the membrane surface. We propose that the lipid order disruption and surface-induced beta-sheet formation on the lipid domain boundary represent the early molecular events of membrane damage associated with the early pathogenesis of T2D.
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Affiliation(s)
- Amber Lewis
- Neuroscience Dept., Trinity University, San Antonio, TX, USA
| | - Thuong Pham
- Physics Dept., Trinity University, San Antonio, TX, USA
| | - Ngoc Nguyen
- Physics Dept., Trinity University, San Antonio, TX, USA
| | - Angela Graf
- Physics Dept., Trinity University, San Antonio, TX, USA
| | - Kwan H Cheng
- Neuroscience Dept., Trinity University, San Antonio, TX, USA; Physics Dept., Trinity University, San Antonio, TX, USA.
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Li Y, Yang M, Nan Y, Wang J, Wang S, Cui D, Guo J, He P, Dai W, Zhou S, Zhang Y, Ma W. SARS-CoV-2 spike host cell surface exposure promoted by a COPI sorting inhibitor. Acta Pharm Sin B 2023:S2211-3835(23)00123-5. [PMID: 37360012 PMCID: PMC10110937 DOI: 10.1016/j.apsb.2023.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/26/2023] [Accepted: 04/10/2023] [Indexed: 06/28/2023] Open
Abstract
Via an insufficient coat protein complex I (COPI) retrieval signal, the majority of SARS-CoV-2 spike (S) is resident in host early secretory organelles and a tiny amount is leaked out in cell surface. Only surface-exposed S can be recognized by B cell receptor (BCR) or anti-S therapeutic monoclonal antibodies (mAbs) that is the trigger step for B cell activation after S mRNA vaccination or infected cell clearance by S mAbs. Now, a drug strategy to promote S host surface exposure is absent. Here, we first combined structural and biochemical analysis to characterize S COPI sorting signals. A potent S COPI sorting inhibitor was then invented, evidently capable of promoting S surface exposure and facilitating infected cell clearance by S antibody-dependent cellular cytotoxicity (ADCC). Importantly, with the inhibitor as a probe, we revealed Omicron BA.1 S is less cell surface exposed than prototypes because of a constellation of S folding mutations, possibly corresponding to its ER chaperone association. Our findings not only suggest COPI is a druggable target against COVID-19, but also highlight SARS-CoV-2 evolution mechanism driven by S folding and trafficking mutations.
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Affiliation(s)
- Yiqun Li
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Mingrui Yang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yanan Nan
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Jiaming Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Sanjiao Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Dongxiao Cui
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Jiajian Guo
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Pengfei He
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Wenxin Dai
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Shuqi Zhou
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yue Zhang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Wenfu Ma
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
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50
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Kocatürk B. In silico analysis reveals PRDX4 as a prognostic and oncogenic marker in renal papillary cell carcinoma. Gene 2023; 859:147201. [PMID: 36646187 DOI: 10.1016/j.gene.2023.147201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/14/2023]
Abstract
BACKGROUND Alterations in the tumor microenvironment leads to the accumulation of reactive oxygen species (ROS). When in low levels, ROS act as a signaling molecule and contribute to tumor cell proliferation whereas its elevation results in oxidative stress and eventually cell death. It is known that antioxidant systems regulate the ROS levels and thus cell fate. Among these systems, peroxiredoxins (PRDXs) were found to be upregulated in various cancers. However their exact contribution to carcinogenesis is not yet clear. AIM Herein, the expression pattern and prognostic value of PRDXs were explored in cancer setting by using in silico analysis tools and publicly available datasets. RESULTS Pan-cancer analysis revealed that PRDXs are differentially expressed in normal and tumor tissues. Further analysis showed that higher PRDX4 levels was associated with poor prognosis and clinicopathological and histological features associated with a more aggressive renal papillary cell carcinoma (KIRP) profile. Hypoxia, ER stress and protein folding were shown to be pathways positively correlated with PRDX4 levels. Furthermore, PRDX4 was found to be strong regulator of protein homeostasis. Kaplan-Meier analysis revealed that PRDX4 is a potent prognostic marker in Type 2 KIRP and this might be due to increased ER stress and oxidative stress levels in this subtype. CONCLUSIONS The data suggest that PRDX4 can be used as a prognostic marker for KIRP patients. Its association with more aggressive tumor characteristics also underlines that it might be used for targeted therapy.
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