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Sola Fraca D, Sánchez Garrigós E, de Francisco Moure J, Marín Gonzalez B, Badiola Díez JJ, Acín Tresaco C. Sleep disturbance in clinical and preclinical scrapie-infected sheep measured by polysomnography. Vet Q 2024; 44:1-9. [PMID: 38698657 PMCID: PMC11073408 DOI: 10.1080/01652176.2024.2349674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/25/2024] [Indexed: 05/05/2024] Open
Abstract
Neurodegenerative diseases are characterised by neuronal loss and abnormal deposition of pathological proteins in the nervous system. Among the most common neurodegenerative diseases are Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease and transmissible spongiform encephalopathies (TSEs). Sleep and circadian rhythm disturbances are one of the most common symptoms in patients with neurodegenerative diseases. Currently, one of the main objectives in the study of TSEs is to try to establish an early diagnosis, as clinical signs do not appear until the damage to the central nervous system is very advanced, which prevents any therapeutic approach. In this paper, we provide the first description of sleep disturbance caused by classical scrapie in clinical and preclinical sheep using polysomnography compared to healthy controls. Fifteen sheep classified into three groups, clinical, preclinical and negative control, were analysed. The results show a decrease in total sleep time as the disease progresses, with significant changes between control, clinical and pre-clinical animals. The results also show an increase in sleep fragmentation in clinical animals compared to preclinical and control animals. In addition, sheep with clinical scrapie show a total loss of Rapid Eye Movement sleep (REM) and alterations in Non Rapid Eyes Movement sleep (NREM) compared to control sheep, demonstrating more shallow sleep. Although further research is needed, these results suggest that prion diseases also produce sleep disturbances in animals and that polysomnography could be a diagnostic tool of interest in clinical and preclinical cases of prion diseases.
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Affiliation(s)
- Diego Sola Fraca
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Universidad de Zaragoza, IA2, IIS Aragón, Zaragoza, Spain
| | | | | | - Belén Marín Gonzalez
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Universidad de Zaragoza, IA2, IIS Aragón, Zaragoza, Spain
| | - Juan José Badiola Díez
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Universidad de Zaragoza, IA2, IIS Aragón, Zaragoza, Spain
| | - Cristina Acín Tresaco
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Universidad de Zaragoza, IA2, IIS Aragón, Zaragoza, Spain
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2
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Deng JL, Huang LF, Bian ZY, Feng XY, Qi RY, Dong WX, Gao JM, Tang JJ. A new neuroprotective candidate TJ1 targeting amyloidogenesis in 5xFAD Alzheimer's disease mice. Int Immunopharmacol 2024; 138:112653. [PMID: 38996664 DOI: 10.1016/j.intimp.2024.112653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/27/2024] [Accepted: 07/06/2024] [Indexed: 07/14/2024]
Abstract
As one of the main pathmechanisms of Alzheimer's disease (AD), amyloid-β (Aβ) is widely considered to be the prime target for the development of AD therapy. Recently, imidazolylacetophenone oxime ethers or esters (IOEs) have shown neuroprotective effects against neuronal cells damage, suggesting their potential use in the prevention and treatment of AD. Thirty IOEs compounds from our lab in-house library were constructed and screened for the inhibitory effects on Aβ42-induced cytotoxicity. Among them, TJ1, as a new IOEs hit, preliminarily showed the effect on inhibiting Aβ42-induced cytotoxicity. Furthermore, the inhibitory effects of TJ1 on Aβ42 aggregation were tested by ThT assays and TEM. The neuroprotective effects of TJ1 were evaluated in Aβ42-stimulated SH-SY5Y cells, LPS-stimulated BV-2 cells, and H2O2- and RSL3-stimulated PC12 cells. The cognitive improvement of TJ1 was assessed in 5xFAD (C57BL/6J) transgenic mouse. These results showed that TJ1 had strong neuroprotective effects and high blood-brain barrier (BBB) permeability without obvious cytotoxicity. TJ1 impeded the self-accumulation process of Aβ42 by acting on Aβ oligomerization and fibrilization. Besides, TJ1 reversed Aβ-, H2O2- and RSL3-induced neuronal cell damage and decreased neuroinflammation. In 5xFAD mice, TJ1 improved cognitive impairment, increased GSH level, reduced the level of Aβ42 and Aβ plaques, and attenuated the glia reactivation and inflammatory response in the brain,. Taken together, our results demonstrate that TJ1 improves cognitive impairments as a new neuroprotective candidate via targeting amyloidogenesis, which suggests the potential of TJ1 as a treatment for AD.
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Affiliation(s)
- Jia-Le Deng
- Shaanxi Key Laboratory of Natural Products and Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Lan-Fang Huang
- Shaanxi Key Laboratory of Natural Products and Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Zhao-Yuan Bian
- Shaanxi Key Laboratory of Natural Products and Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Xu-Yao Feng
- Shaanxi Key Laboratory of Natural Products and Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Ruo-Yu Qi
- Shaanxi Key Laboratory of Natural Products and Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Wei-Xuan Dong
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710000, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products and Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Jiang-Jiang Tang
- Shaanxi Key Laboratory of Natural Products and Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, 712100, China.
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3
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Dasari AKR, Coats MF, Ali AB, Lim KH. Identification of the interfacial regions in misfolded transthyretin oligomers. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141027. [PMID: 38796131 PMCID: PMC11283945 DOI: 10.1016/j.bbapap.2024.141027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/14/2024] [Accepted: 05/22/2024] [Indexed: 05/28/2024]
Abstract
Misfolding and aggregation of transthyretin (TTR) is associated with numerous ATTR amyloidosis. TTR aggregates extracted from ATTR patients consist of not only full-length TTR, but also N-terminally truncated TTR fragments that can be produced by proteolytic cleavage, suggesting the presence of multiple misfolding pathways. Here, we report mechanistic studies of an early stage of TTR aggregation to probe the oligomerization process for the full-length as well as N-terminally truncated TTR. Our kinetic analyses using size exclusion chromatography revealed that amyloidogenic monomers dissociated from wild-type (WT) as well as pathogenic variants (V30M and L55P) form misfolded dimers, which self-assemble into oligomers, precursors of fibril formation. Dimeric interfaces in the full-length misfolded oligomers were investigated by examining the effect of single-point mutations on the two β-strands (F and H). The single-point mutations on the two β-strands (E92P on strand F and T119W on strand H) inhibited the dimerization of misfolded monomers, while the TTR variants can still form native dimers through the same F and H strands. These results suggest that the two strands are involved in intermolecular associations for both native and misfolded dimers, but detailed intermolecular interactions are different in the two forms of dimers. In the presence of a proteolytic enzyme, TTR aggregation is greatly accelerated. The two mutations on the two β-strands, however, inhibited TTR aggregation even in the presence of a proteolytic enzyme, trypsin. These results suggest that the two β-strands (F and H) play a critical role in aggregation of the N-terminally truncated TTR as well.
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Affiliation(s)
- Anvesh K R Dasari
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Matthew F Coats
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | | | - Kwang Hun Lim
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA.
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Esposito A, Leone L, De Simone A, Fusco G, Nastri F, Lombardi A. Catalytic Nanomaterials by Conjugation of an Artificial Heme-Peroxidase to Amyloid Fibrils. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 39140178 DOI: 10.1021/acsami.4c10449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
The self-assembly of proteins and peptides into fibrillar amyloid aggregates is a highly promising route to define the next generation of functional nanomaterials. Amyloid fibrils, traditionally associated with neurodegenerative diseases, offer exceptional conformational and chemical stability and mechanical properties, and resistance to degradation. Here, we report the development of catalytic amyloid nanomaterials through the conjugation of a miniaturized artificial peroxidase (FeMC6*a) to a self-assembling amyloidogenic peptide derived from human transthyretin, TTR(105-115), whose sequence is YTIAALLSPYS. Our synthetic approach relies on fast and selective click ligation upon proper modification of both the peptide and FeMC6*a, leading to TTRLys108@FeMC6*a. Mixing unmodified TTR(105-115) with TTRLys108@FeMC6*a allowed the generation of enzyme-loaded amyloid fibrils, namely, FeMC6*a@fibrils. Catalytic studies, performed in aqueous solution at nearly neutral pH, using ABTS as a model substrate and H2O2 as the oxidizing agent revealed that the enzyme retains its catalytic activity. Moreover, the activity was found to depend on the TTRLys108@FeMC6*a/unmodified TTR(105-115) peptide ratio. In particular, those with the 2:100 ratio showed the highest activity in terms of initial rates and substrate conversion among the screened nanoconjugates and compared to the freely diffusing enzyme. Finally, the newly developed nanomaterials were integrated into a flow system based on a polyvinylidene difluoride membrane filter. Within this flow-reactor, multiple reaction cycles were performed, showcasing the reusability and stability of the catalytic amyloids over extended periods, thus offering significantly improved characteristics compared to the isolated FeMC6*a in the application to a number of practical scenarios.
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Affiliation(s)
- Alessandra Esposito
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126 Naples, Italy
| | - Linda Leone
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126 Naples, Italy
| | - Alfonso De Simone
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Giuliana Fusco
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126 Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126 Naples, Italy
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Suzuki K, Nojiri R, Matsusaki M, Mabuchi T, Kanemura S, Ishii K, Kumeta H, Okumura M, Saio T, Muraoka T. Redox-active chemical chaperones exhibiting promiscuous binding promote oxidative protein folding under condensed sub-millimolar conditions. Chem Sci 2024; 15:12676-12685. [PMID: 39148798 PMCID: PMC11323320 DOI: 10.1039/d4sc02123a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 07/09/2024] [Indexed: 08/17/2024] Open
Abstract
Proteins form native structures through folding processes, many of which proceed through intramolecular hydrophobic effect, hydrogen bond and disulfide-bond formation. In vivo, protein aggregation is prevented even in the highly condensed milieu of a cell through folding mediated by molecular chaperones and oxidative enzymes. Chemical approaches to date have not replicated such exquisite mediation. Oxidoreductases efficiently promote folding by the cooperative effects of oxidative reactivity for disulfide-bond formation in the client unfolded protein and chaperone activity to mitigate aggregation. Conventional synthetic folding promotors mimic the redox-reactivity of thiol/disulfide units but do not address client-recognition units for inhibiting aggregation. Herein, we report thiol/disulfide compounds containing client-recognition units, which act as synthetic oxidoreductase-mimics. For example, compound βCDWSH/SS bears a thiol/disulfide unit at the wide rim of β-cyclodextrin as a client recognition unit. βCDWSH/SS shows promiscuous binding to client proteins, mitigates protein aggregation, and accelerates disulfide-bond formation. In contrast, positioning a thiol/disulfide unit at the narrow rim of β-cyclodextrin promotes folding less effectively through preferential interactions at specific residues, resulting in aggregation. The combination of promiscuous client-binding and redox reactivity is effective for the design of synthetic folding promoters. βCDWSH/SS accelerates oxidative protein folding at highly condensed sub-millimolar protein concentrations.
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Affiliation(s)
- Koki Suzuki
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology Koganei Tokyo 184-8588 Japan
| | - Ryoya Nojiri
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology Koganei Tokyo 184-8588 Japan
| | - Motonori Matsusaki
- Division of Molecular Life Science, Institute of Advanced Medical Sciences, Tokushima University Tokushima 770-8503 Japan
| | - Takuya Mabuchi
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University Sendai Miyagi 980-8578 Japan
- Institute of Fluid Science, Tohoku University Sendai Miyagi 980-8577 Japan
| | - Shingo Kanemura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University Sendai Miyagi 980-8578 Japan
| | - Kotone Ishii
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University Sendai Miyagi 980-8578 Japan
| | - Hiroyuki Kumeta
- Faculty of Advanced Life Science, Hokkaido University Sapporo Hokkaido 060-0810 Japan
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University Sendai Miyagi 980-8578 Japan
| | - Tomohide Saio
- Division of Molecular Life Science, Institute of Advanced Medical Sciences, Tokushima University Tokushima 770-8503 Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology Koganei Tokyo 184-8588 Japan
- Kanagawa Institute of Industrial Science and Technology (KISTEC) Kanagawa 243-0435 Japan
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6
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Qi X, Lv X, Pan W, Shen M, Chen Y, Yu Q, Xie J. Antioxidant amyloid fibril derived from rice protein hydrolysate as stabilizer towards preparing high-stable emulsion. Food Chem 2024; 460:140745. [PMID: 39126945 DOI: 10.1016/j.foodchem.2024.140745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/02/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024]
Abstract
An antioxidant amyloid fibril was prepared as an emulsifier by fibrillating limited enzymatic hydrolysis-modified rice protein (HRP). The purpose of this study was to investigate the feasibility of using fibrillated HRP to stabilize oil-in-water emulsion. A free radical scavenging assay revealed that the antioxidant activity of fibrillated HRP was 2.09 times higher than that of native rice protein. Fibrillated HRP demonstrated a marked reduction in interfacial tension, increased surface hydrophobicity and contact angle (> 80°), and rapid adsorption to the interface, with 35.34 ± 2.43% interfacial adsorbed protein content. The fibrillated HRP barriers resisted environment stresses such as NaCl, pH variations, long-term storage, while reducing lipid oxidation degree. Additionally, fibrillated HRP-based emulsion was more effective in protecting β-carotene from degradation compared to other samples. These findings provide theoretical support for the development of rice protein-based antioxidant emulsifiers and modification of emulsifying properties of plant proteins.
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Affiliation(s)
- Xin Qi
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Xinyu Lv
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Wentao Pan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Mingyue Shen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Yi Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Qiang Yu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Jianhua Xie
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China.
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7
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Stavgiannoudaki I, Goulielmaki E, Garinis GA. Broken strands, broken minds: Exploring the nexus of DNA damage and neurodegeneration. DNA Repair (Amst) 2024; 140:103699. [PMID: 38852477 DOI: 10.1016/j.dnarep.2024.103699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/15/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
Neurodegenerative disorders are primarily characterized by neuron loss progressively leading to cognitive decline and the manifestation of incurable and debilitating conditions, such as Alzheimer's, Parkinson's, and Huntington's diseases. Loss of genome maintenance causally contributes to age-related neurodegeneration, as exemplified by the premature appearance of neurodegenerative features in a growing family of human syndromes and mice harbouring inborn defects in DNA repair. Here, we discuss the relevance of persistent DNA damage, key DNA repair mechanisms and compromised genome integrity in age-related neurodegeneration highlighting the significance of investigating these connections to pave the way for the development of rationalized intervention strategies aimed at delaying the onset of neurodegenerative disorders and promoting healthy aging.
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Affiliation(s)
- Ioanna Stavgiannoudaki
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Crete, Heraklion, Greece; Department of Biology, University of Crete, Crete, Heraklion, Greece
| | - Evi Goulielmaki
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Crete, Heraklion, Greece
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Crete, Heraklion, Greece; Department of Biology, University of Crete, Crete, Heraklion, Greece.
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Chuan J, Li W, Pan S, Jiang Z, Shi J, Yang Z. Progress in the development of modulators targeting Frizzleds. Pharmacol Res 2024; 206:107286. [PMID: 38936522 DOI: 10.1016/j.phrs.2024.107286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/08/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
The Frizzleds (FZDs) receptors on the cell surface belong to the class F of G protein-coupled receptors (GPCRs) which are the major receptors of WNT protein that mediates the classical WNT signaling pathway and other non-classical pathways. Besides, the FZDs also play a core role in tissue regeneration and tumor occurrence. With the structure and mechanism of FZDs activation becoming clearer, a series of FZDs modulators (inhibitors and agonists) have been developed, with the hope of bringing benefits to the treatment of cancer and degenerative diseases. Most of the FZDs inhibitors (small molecules, antibodies or designed protein inhibitors) block WNT signaling through binding to the cysteine-rich domain (CRD) of FZDs. Several small molecules impede FZDs activation by targeting to the third intracellular domain or the transmembrane domain of FZDs. However, three small molecules (FZM1.8, SAG1.3 and purmorphamine) activate the FZDs through direct interaction with the transmembrane domain. Another type of FZDs agonists are bivalent or tetravalent antibodies which activate the WNT signaling via inducing FZD-LRP5/6 heterodimerization. In this article, we reviewed the FZDs modulators reported in recent years, summarized the critical molecules' discovery processes and the elucidated relevant structural and pharmacological mechanisms. We believe the summaried molecular mechanisms of the relevant modulators could provide important guidance and reference for the future development of FZD modulators.
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Affiliation(s)
- Junlan Chuan
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Wei Li
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu 610041, China; The University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101408, China
| | - Shengliu Pan
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu 610041, China; The University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101408, China
| | - Zhongliang Jiang
- Hematology Department, Miller School of Medicine, University of Miami, USA
| | - Jianyou Shi
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.
| | - Zhenglin Yang
- Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China; Jinfeng Laboratory, Chongqing, China.
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9
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Vila JA. Analysis of proteins in the light of mutations. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:255-265. [PMID: 38955858 DOI: 10.1007/s00249-024-01714-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 07/04/2024]
Abstract
Proteins have evolved through mutations-amino acid substitutions-since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function, and structure. This study offers a new viewpoint on how the most recent findings in these areas can be used to explore the impact of mutations on protein sequence, stability, and evolvability. Preliminary results indicate that: (1) mutations can be viewed as sensitive probes to identify 'typos' in the amino-acid sequence, and also to assess the resistance of naturally occurring proteins to unwanted sequence alterations; (2) the presence of 'typos' in the amino acid sequence, rather than being an evolutionary obstacle, could promote faster evolvability and, in turn, increase the likelihood of higher protein stability; (3) the mutation site is far more important than the substituted amino acid in terms of the marginal stability changes of the protein, and (4) the unpredictability of protein evolution at the molecular level-by mutations-exists even in the absence of epistasis effects. Finally, the Darwinian concept of evolution "descent with modification" and experimental evidence endorse one of the results of this study, which suggests that some regions of any protein sequence are susceptible to mutations while others are not. This work contributes to our general understanding of protein responses to mutations and may spur significant progress in our efforts to develop methods to accurately forecast changes in protein stability, their propensity for metamorphism, and their ability to evolve.
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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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10
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Shamim S, Mohsin AS, Rahman MM, Hossain Bhuian MB. Recent advances in the metamaterial and metasurface-based biosensor in the gigahertz, terahertz, and optical frequency domains. Heliyon 2024; 10:e33272. [PMID: 39040247 PMCID: PMC11260956 DOI: 10.1016/j.heliyon.2024.e33272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/24/2024] Open
Abstract
Recently, metamaterials and metasurface have gained rapidly increasing attention from researchers due to their extraordinary optical and electrical properties. Metamaterials are described as artificially defined periodic structures exhibiting negative permittivity and permeability simultaneously. Whereas metasurfaces are the 2D analogue of metamaterials in the sense that they have a small but not insignificant depth. Because of their high optical confinement and adjustable optical resonances, these artificially engineered materials appear as a viable photonic platform for biosensing applications. This review paper discusses the recent development of metamaterial and metasurface in biosensing applications based on the gigahertz, terahertz, and optical frequency domains encompassing the whole electromagnetic spectrum. Overlapping features such as material selection, structure, and physical mechanisms were considered during the classification of our biosensing applications. Metamaterials and metasurfaces working in the GHz range provide prospects for better sensing of biological samples, THz frequencies, falling between GHz and optical frequencies, provide unique characteristics for biosensing permitting the exact characterization of molecular vibrations, with an emphasis on molecular identification, label-free analysis, and imaging of biological materials. Optical frequencies on the other hand cover the visible and near-infrared regions, allowing fine regulation of light-matter interactions enabling metamaterials and metasurfaces to offer excellent sensitivity and specificity in biosensing. The outcome of the sensor's sensitivity to an electric or magnetic field and the resonance frequency are, in theory, determined by the frequency domain and features. Finally, the challenges and possible future perspectives in biosensing application areas have been presented that use metamaterials and metasurfaces across diverse frequency domains to improve sensitivity, specificity, and selectivity in biosensing applications.
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Affiliation(s)
- Shadmani Shamim
- Department of Electrical and Electronic Engineering, Optics and Photonics Research Group, BRAC University, Kha 224 Bir Uttam Rafiqul Islam Avenue, Merul Badda, Dhaka 1212, Bangladesh
| | - Abu S.M. Mohsin
- Department of Electrical and Electronic Engineering, Optics and Photonics Research Group, BRAC University, Kha 224 Bir Uttam Rafiqul Islam Avenue, Merul Badda, Dhaka 1212, Bangladesh
| | - Md. Mosaddequr Rahman
- Department of Electrical and Electronic Engineering, Optics and Photonics Research Group, BRAC University, Kha 224 Bir Uttam Rafiqul Islam Avenue, Merul Badda, Dhaka 1212, Bangladesh
| | - Mohammed Belal Hossain Bhuian
- Department of Electrical and Electronic Engineering, Optics and Photonics Research Group, BRAC University, Kha 224 Bir Uttam Rafiqul Islam Avenue, Merul Badda, Dhaka 1212, Bangladesh
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11
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Lee E, Park H, Kim S. Transcellular transmission and molecular heterogeneity of aggregation-prone proteins in neurodegenerative diseases. Mol Cells 2024; 47:100089. [PMID: 38971320 PMCID: PMC11286998 DOI: 10.1016/j.mocell.2024.100089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024] Open
Abstract
The accumulation of aggregation-prone proteins in a specific neuronal population is a common feature of neurodegenerative diseases, which is correlated with the development of pathological lesions in diseased brains. The formation and progression of pathological protein aggregates in susceptible neurons induce cellular dysfunction, resulting in progressive degeneration. Moreover, recent evidence supports the notion that the cell-to-cell transmission of pathological protein aggregates may be involved in the onset and progression of many neurodegenerative diseases. Indeed, several studies have identified different pathological aggregate strains. Although how these different aggregate strains form remains unclear, a variety of biomolecular compositions or cross-seeding events promoted by the presence of other protein aggregates in the cellular environment may affect the formation of different strains of pathological aggregates, which in turn can influence complex pathologies in diseased brains. In this review, we summarize the recent results regarding cell-to-cell transmission and the molecular heterogeneity of pathological aggregate strains, raising key questions for future research directions.
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Affiliation(s)
- Eunmin Lee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644, Korea
| | - Hyeonwoo Park
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644, Korea
| | - Sangjune Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644, Korea.
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Aranda-Anzaldo A, Dent MAR, Segura-Anaya E, Martínez-Gómez A. Protein folding, cellular stress and cancer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 191:40-57. [PMID: 38969306 DOI: 10.1016/j.pbiomolbio.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Proteins are acknowledged as the phenotypical manifestation of the genotype, because protein-coding genes carry the information for the strings of amino acids that constitute the proteins. It is widely accepted that protein function depends on the corresponding "native" structure or folding achieved within the cell, and that native protein folding corresponds to the lowest free energy minimum for a given protein. However, protein folding within the cell is a non-deterministic dissipative process that from the same input may produce different outcomes, thus conformational heterogeneity of folded proteins is the rule and not the exception. Local changes in the intracellular environment promote variation in protein folding. Hence protein folding requires "supervision" by a host of chaperones and co-chaperones that help their client proteins to achieve the folding that is most stable according to the local environment. Such environmental influence on protein folding is continuously transduced with the help of the cellular stress responses (CSRs) and this may lead to changes in the rules of engagement between proteins, so that the corresponding protein interactome could be modified by the environment leading to an alternative cellular phenotype. This allows for a phenotypic plasticity useful for adapting to sudden and/or transient environmental changes at the cellular level. Starting from this perspective, hereunder we develop the argument that the presence of sustained cellular stress coupled to efficient CSRs may lead to the selection of an aberrant phenotype as the resulting adaptation of the cellular proteome (and the corresponding interactome) to such stressful conditions, and this can be a common epigenetic pathway to cancer.
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Affiliation(s)
- Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, 50180, Edo. Méx., Mexico.
| | - Myrna A R Dent
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, 50180, Edo. Méx., Mexico
| | - Edith Segura-Anaya
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, 50180, Edo. Méx., Mexico
| | - Alejandro Martínez-Gómez
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, 50180, Edo. Méx., Mexico
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13
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Levine H, Tu Y. Machine learning meets physics: A two-way street. Proc Natl Acad Sci U S A 2024; 121:e2403580121. [PMID: 38913898 PMCID: PMC11228530 DOI: 10.1073/pnas.2403580121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024] Open
Affiliation(s)
- Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02115
| | - Yuhai Tu
- IBM T. J. Watson Research Center, Yorktown Heights, New York, NY 10598
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Hüper L, Steinacker P, Polyakova M, Mueller K, Godulla J, Herzig S, Danek A, Engel A, Diehl‐Schmid J, Classen J, Fassbender K, Fliessbach K, Jahn H, Kassubek J, Kornhuber J, Landwehrmeyer B, Lauer M, Obrig H, Oeckl P, Prudlo J, Saur D, Anderl‐Straub S, Synofzik M, Wagner M, Wiltfang J, Winkelmann J, Volk AE, Huppertz H, Otto M, Schroeter ML. Neurofilaments and progranulin are related to atrophy in frontotemporal lobar degeneration - A transdiagnostic study cross-validating atrophy and fluid biomarkers. Alzheimers Dement 2024; 20:4461-4475. [PMID: 38865340 PMCID: PMC11247715 DOI: 10.1002/alz.13863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 06/14/2024]
Abstract
INTRODUCTION Frontotemporal lobar degeneration (FTLD) encompasses behavioral variant frontotemporal dementia (bvFTD), progressive supranuclear palsy, corticobasal syndrome/degeneration, and primary progressive aphasias (PPAs). We cross-validated fluid biomarkers and neuroimaging. METHODS Seven fluid biomarkers from cerebrospinal fluid and serum were related to atrophy in 428 participants including these FTLD subtypes, logopenic variant PPA (lvPPA), Alzheimer's disease (AD), and healthy subjects. Atrophy was assessed by structural magnetic resonance imaging and atlas-based volumetry. RESULTS FTLD subtypes, lvPPA, and AD showed specific profiles for neurofilament light chain, phosphorylated heavy chain, tau, phospho-tau, amyloid beta1-42 from serum/cerebrospinal fluid, and brain atrophy. Neurofilaments related to regional atrophy in bvFTD, whereas progranulin was associated with atrophy in semantic variant PPA. Ubiquitin showed no effects. DISCUSSION Results specify biomarker and atrophy patterns in FTLD and AD supporting differential diagnosis. They identify neurofilaments and progranulin in interaction with structural imaging as promising candidates for monitoring disease progression and therapy. HIGHLIGHTS Study cross-validated neuroimaging and fluid biomarkers in dementia. Five kinds of frontotemporal lobar degeneration and two variants of Alzheimer's disease. Study identifies disease-specific fluid biomarker and atrophy profiles. Fluid biomarkers and atrophy interact in a disease-specific way. Neurofilaments and progranulin are proposed as biomarkers for diagnosis and therapy.
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Chang CY, Wang SSS, Lai YR, Koh WG, Wu JW, Chiang YH. Ophthalmic drug effects on the amyloidogenesis of a transforming growth factor β-induced protein (TGFBIp) peptide fragment. Exp Eye Res 2024; 244:109932. [PMID: 38762008 DOI: 10.1016/j.exer.2024.109932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 03/30/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024]
Abstract
Drugs that can treat one disease may either be detrimental or beneficial toward another due to possible cross-interactions. Therefore, care in choosing a suitable drug for patients with multiple diseases is crucial in successful patient management. This study explores several currently available ophthalmic drugs used to treat common ocular diseases to understand how they can affect the amyloidogenesis of a transforming growth factor β-induced protein (TGFBIp) peptide fragment found in abundance in the corneal protein aggregation deposits of lattice corneal dystrophy (LCD) patients. Results from this study provided supporting evidence that some drugs intended to treat other diseases can enhance or inhibit fibrillar aggregation of TGFBIp peptide, which may have potential implication of affecting the disease progression of LCD by either worsening or ameliorating it. Comparisons of the different properties of ophthalmic compounds explored in this study may also provide some guidance for future design of drugs geared toward the treatment of LCD.
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Affiliation(s)
- Chia-Yu Chang
- Department of Chemical Engineering, National Taiwan University, Taipei, 10617, Taiwan
| | - Steven S-S Wang
- Department of Chemical Engineering, National Taiwan University, Taipei, 10617, Taiwan
| | - You-Ren Lai
- Department of Chemical Engineering, National Taiwan University, Taipei, 10617, Taiwan
| | - Won-Gun Koh
- Department of Chemical and Biomolecular Engineering, Yonsei University, South Korea
| | - Josephine W Wu
- Department of Optometry, Yuanpei University of Medical Technology, Hsinchu City, 30015, Taiwan; Department of Optometry, Mackay Medical College, New Taipei City, 252, Taiwan.
| | - Yi-Hui Chiang
- Department of Ophthalmology, En Chu Kong Hospital, New Taipei City, 237, Taiwan.
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16
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de Boni L, Wallis A, Hays Watson A, Ruiz-Riquelme A, Leyland LA, Bourinaris T, Hannaway N, Wüllner U, Peters O, Priller J, Falkenburger BH, Wiltfang J, Bähr M, Zerr I, Bürger K, Perneczky R, Teipel S, Löhle M, Hermann W, Schott BH, Brockmann K, Spottke A, Haustein K, Breuer P, Houlden H, Weil RS, Bartels T. Aggregation-resistant alpha-synuclein tetramers are reduced in the blood of Parkinson's patients. EMBO Mol Med 2024; 16:1657-1674. [PMID: 38839930 PMCID: PMC11250827 DOI: 10.1038/s44321-024-00083-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/02/2024] [Accepted: 05/17/2024] [Indexed: 06/07/2024] Open
Abstract
Synucleinopathies such as Parkinson's disease (PD) are defined by the accumulation and aggregation of the α-synuclein protein in neurons, glia and other tissues. We have previously shown that destabilization of α-synuclein tetramers is associated with familial PD due to SNCA mutations and demonstrated brain-region specific alterations of α-synuclein multimers in sporadic PD patients following the classical Braak spreading theory. In this study, we assessed relative levels of disordered and higher-ordered multimeric forms of cytosolic α-synuclein in blood from familial PD with G51D mutations and sporadic PD patients. We used an adapted in vitro-cross-linking protocol for human EDTA-whole blood. The relative levels of higher-ordered α-synuclein tetramers were diminished in blood from familial PD and sporadic PD patients compared to controls. Interestingly, the relative amount of α-synuclein tetramers was already decreased in asymptomatic G51D carriers, supporting the hypothesis that α-synuclein multimer destabilization precedes the development of clinical PD. Our data, therefore suggest that measuring α-synuclein tetramers in blood may have potential as a facile biomarker assay for early detection and quantitative tracking of PD progression.
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Affiliation(s)
- Laura de Boni
- UK Dementia Research Institute, University College London, London, W1T 7NF, UK
- Institute of Aerospace Medicine, German Aerospace Center (DLR), 51147, Cologne, Germany
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany
| | - Amber Wallis
- UK Dementia Research Institute, University College London, London, W1T 7NF, UK
| | - Aurelia Hays Watson
- UK Dementia Research Institute, University College London, London, W1T 7NF, UK
| | | | - Louise-Ann Leyland
- Dementia Research Center, Institute of Neurology, University College London, Queen Square, London, WC1N 3BG, UK
| | - Thomas Bourinaris
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Naomi Hannaway
- Dementia Research Center, Institute of Neurology, University College London, Queen Square, London, WC1N 3BG, UK
| | - Ullrich Wüllner
- German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
- Departments of Neurology and Neurodegenerative Diseases, University Bonn, 53127, Bonn, Germany
| | - Oliver Peters
- Institute of Psychiatry and Psychotherapy, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), 10117, Berlin, Germany
| | - Josef Priller
- German Center for Neurodegenerative Diseases (DZNE), 10117, Berlin, Germany
- Department of Psychiatry and Psychotherapy, Charité, Charitéplatz 1, 10117, Berlin, Germany
- University of Edinburgh and UK DRI, Edinburgh, EH16 4SB, UK
- School of Medicine, Technical University of Munich, Department of Psychiatry and Psychotherapy, 81675, Munich, Germany
| | - Björn H Falkenburger
- German Center for Neurodegenerative Diseases (DZNE), 01307, Dresden, Germany
- Department of Neurology, University Hospital Carl Gustav Carus, Dresden University of Technology, 01307, Dresden, Germany
| | - Jens Wiltfang
- German Center for Neurodegenerative Diseases (DZNE), 37075, Goettingen, Germany
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen, Georg August University, 37075, Göttingen, Germany
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Mathias Bähr
- German Center for Neurodegenerative Diseases (DZNE), 37075, Goettingen, Germany
- Department of Neurology, University Medical Center, Georg August University, 37075, Göttingen, Germany
- Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Inga Zerr
- German Center for Neurodegenerative Diseases (DZNE), 37075, Goettingen, Germany
- Department of Neurology, University Medical Center, Georg August University, 37075, Göttingen, Germany
| | - Katharina Bürger
- German Center for Neurodegenerative Diseases (DZNE), 81377, Munich, Germany
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Robert Perneczky
- German Center for Neurodegenerative Diseases (DZNE), 81377, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, 81377, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy) Munich, 81377, Munich, Germany
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College London, London, W6 8RP, UK
| | - Stefan Teipel
- German Center for Neurodegenerative Diseases (DZNE), Rostock-Greifswald, 17489, Rostock, Germany
- Department of Psychosomatic Medicine, Rostock University Medical Center, 18147, Rostock, Germany
| | - Matthias Löhle
- German Center for Neurodegenerative Diseases (DZNE), Rostock-Greifswald, 17489, Rostock, Germany
- Department of Neurology, University of Rostock, 18057, Rostock, Germany
| | - Wiebke Hermann
- German Center for Neurodegenerative Diseases (DZNE), Rostock-Greifswald, 17489, Rostock, Germany
- Department of Neurology, University of Rostock, 18057, Rostock, Germany
| | - Björn-Hendrik Schott
- German Center for Neurodegenerative Diseases (DZNE), 37075, Goettingen, Germany
- Department of Psychiatry and Psychotherapy, University Hospital Göttingen, Georg August University, 37075, Göttingen, Germany
| | - Kathrin Brockmann
- German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany
- Hertie Institute for Clinical Brain Research, Department of Neurodegenerative Diseases, University of Tübingen, 72076, Tübingen, Germany
| | - Annika Spottke
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
| | - Katrin Haustein
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany
| | - Peter Breuer
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Rimona S Weil
- Dementia Research Center, Institute of Neurology, University College London, Queen Square, London, WC1N 3BG, UK
| | - Tim Bartels
- UK Dementia Research Institute, University College London, London, W1T 7NF, UK.
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Wang X, Feng Y, Wang F, Lin Z, Huang J, Li Q, Luo H, Liu X, Zhai X, Gao Q, Li L, Zhang Y, Wen J, Zhang L, Niu T, Zheng Y. Single-cell sequencing reveals the correlation of aggrephagy signaling and multiple myeloma immune microenvironment composition. J Gene Med 2024; 26:e3712. [PMID: 38949072 DOI: 10.1002/jgm.3712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/07/2023] [Accepted: 06/02/2024] [Indexed: 07/02/2024] Open
Abstract
Aggrephagy, a type of autophagy, degrades the aggregation of misfolded protein in cells. However, the role of aggrephagy in multiple myeloma (MM) has not been fully demonstrated. In this study, we first investigated the correlation between aggrephagy signaling, MM immune microenvironment composition and disease prognosis. Single-cell RNA-seq data, including the expression profiles of 12,187 single cells from seven MM bone marrow (BM) and seven healthy BM samples, were analyzed by non-negative matrix factorization for 44 aggrephagy-related genes. Bulk RNA-seq cohorts from the Gene Expression Omnibus database were used to evaluate the prognostic value of aggrephagy-related immune cell subtypes and predict immune checkpoint blockade immunotherapeutic response in MM. Compared with healthy BM, MM BM exhibited different patterns of aggrephagy-related gene expression. In MM BM, macrophages, CD8+ T cells, B cells and natural killer cells could be grouped into four to nine aggrephagy-related subclusters. The signature of aggrephagy signaling molecule expression in the immune cells correlates with the patient's prognosis. Our investigation provides a novel view of aggrephagy signaling in MM tumor microenvironment cells, which might be a prognostic indicator and potential target for MM treatment.
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Affiliation(s)
- Xin Wang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Feng
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Fangfang Wang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhimei Lin
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
- Department of Hematology, The Affiliated Hospital of Chengdu University, Chengdu, China
| | - Jingcao Huang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Qian Li
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Hongmei Luo
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Xiang Liu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Xinyu Zhai
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Qianwen Gao
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
- School of Life Science, Sichuan University, Chengdu, China
| | - Linfeng Li
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Zhang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Jingjing Wen
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
- Department of Hematology, Mianyang Central Hospital, Mianyang, China
| | - Li Zhang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Ting Niu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Yuhuan Zheng
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
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Morfino P, Aimo A, Franzini M, Vergaro G, Castiglione V, Panichella G, Limongelli G, Emdin M. Pathophysiology of Cardiac Amyloidosis. Heart Fail Clin 2024; 20:261-270. [PMID: 38844297 DOI: 10.1016/j.hfc.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Amyloidosis refers to a heterogeneous group of disorders sharing common pathophysiological mechanisms characterized by the extracellular accumulation of fibrillar deposits consisting of the aggregation of misfolded proteins. Cardiac amyloidosis (CA), usually caused by deposition of misfolded transthyretin or immunoglobulin light chains, is an increasingly recognized cause of heart failure burdened by a poor prognosis. CA manifests with a restrictive cardiomyopathy which progressively leads to biventricular thickening, diastolic and then systolic dysfunction, arrhythmias, and valvular disease. The pathophysiology of CA is multifactorial and includes increased oxidative stress, mitochondrial damage, apoptosis, impaired metabolism, and modifications of intracellular calcium balance.
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Affiliation(s)
| | - Alberto Aimo
- Fondazione Toscana Gabriele Monasterio, via G. Moruzzi 1, 56124, Pisa, Italy; Health Science Interdisciplinary Center, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Maria Franzini
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
| | - Giuseppe Vergaro
- Fondazione Toscana Gabriele Monasterio, via G. Moruzzi 1, 56124, Pisa, Italy; Health Science Interdisciplinary Center, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Vincenzo Castiglione
- Fondazione Toscana Gabriele Monasterio, via G. Moruzzi 1, 56124, Pisa, Italy; Health Science Interdisciplinary Center, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Giorgia Panichella
- Department of Clinical and Experimental Medicine, Careggi University Hospital, Florence, Italy
| | - Giuseppe Limongelli
- Inherited and Rare Cardiovascular Disease Unit, Department of Translational Medical Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Michele Emdin
- Scuola Superiore Sant'Anna, Pisa, Italy; Fondazione Toscana Gabriele Monasterio, via G. Moruzzi 1, 56124, Pisa, Italy.
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Sharma A, Shah OP, Sharma L, Gulati M, Behl T, Khalid A, Mohan S, Najmi A, Zoghebi K. Molecular Chaperones as Therapeutic Target: Hallmark of Neurodegenerative Disorders. Mol Neurobiol 2024; 61:4750-4767. [PMID: 38127187 DOI: 10.1007/s12035-023-03846-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023]
Abstract
Misfolded and aggregated proteins build up in neurodegenerative illnesses, which causes neuronal dysfunction and ultimately neuronal death. In the last few years, there has been a significant upsurge in the level of interest towards the function of molecular chaperones in the control of misfolding and aggregation. The crucial molecular chaperones implicated in neurodegenerative illnesses are covered in this review article, along with a variety of their different methods of action. By aiding in protein folding, avoiding misfolding, and enabling protein breakdown, molecular chaperones serve critical roles in preserving protein homeostasis. By aiding in protein folding, avoiding misfolding, and enabling protein breakdown, molecular chaperones have integral roles in preserving regulation of protein balance. It has been demonstrated that aging, a significant risk factor for neurological disorders, affects how molecular chaperones function. The aggregation of misfolded proteins and the development of neurodegeneration may be facilitated by the aging-related reduction in chaperone activity. Molecular chaperones have also been linked to the pathophysiology of several instances of neuron withering illnesses, enumerating as Parkinson's disease, Huntington's disease, and Alzheimer's disease. Molecular chaperones have become potential therapy targets concerning with the prevention and therapeutic approach for brain disorders due to their crucial function in protein homeostasis and their connection to neurodegenerative illnesses. Protein homeostasis can be restored, and illness progression can be slowed down by methods that increase chaperone function or modify their expression. This review emphasizes the importance of molecular chaperones in the context of neuron withering disorders and their potential as therapeutic targets for brain disorders.
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Affiliation(s)
- Aditi Sharma
- School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Om Prakash Shah
- School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Lalit Sharma
- School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 1444411, India
- ARCCIM, Faculty of Health, University of Technology Sydney, Ultimo, NSW, 20227, Australia
| | - Tapan Behl
- Amity School of Pharmaceutical Sciences, Amity University, Mohali, Punjab, India, Amity University, Mohali, India.
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan, 45142, Saudi Arabia
- Medicinal and Aromatic Plants Research Institute, National Center for Research, P.O. Box 2424, 11111, Khartoum, Sudan
| | - Syam Mohan
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan, 45142, Saudi Arabia.
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India.
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India.
| | - Asim Najmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan, Saudi Arabia
| | - Khalid Zoghebi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan, Saudi Arabia
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20
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Zheng X, Ni Z, Pei Q, Wang M, Tan J, Bai S, Shi F, Ye S. Probing the Molecular Structure and Dynamics of Membrane-Bound Proteins during Misfolding Processes by Sum-Frequency Generation Vibrational Spectroscopy. Chempluschem 2024; 89:e202300684. [PMID: 38380553 DOI: 10.1002/cplu.202300684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 02/22/2024]
Abstract
Protein misfolding and amyloid formation are implicated in the protein dysfunction, but the underlying mechanism remains to be clarified due to the lack of effective tools for detecting the transient intermediates. Sum frequency generation vibrational spectroscopy (SFG-VS) has emerged as a powerful tool for identifying the structure and dynamics of proteins at the interfaces. In this review, we summarize recent SFG-VS studies on the structure and dynamics of membrane-bound proteins during misfolding processes. This paper first introduces the methods for determining the secondary structure of interfacial proteins: combining chiral and achiral spectra of amide A and amide I bands and combining amide I, amide II, and amide III spectral features. To demonstrate the ability of SFG-VS in investigating the interfacial protein misfolding and amyloid formation, studies on the interactions between different peptides/proteins (islet amyloid polypeptide, amyloid β, prion protein, fused in sarcoma protein, hen egg-white lysozyme, fusing fusion peptide, class I hydrophobin SC3 and class II hydrophobin HFBI) and surfaces such as lipid membranes are discussed. These molecular-level studies revealed that SFG-VS can provide a unique understanding of the mechanism of interfacial protein misfolding and amyloid formation in real time, in situ and without any exogenous labeling.
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Affiliation(s)
- Xiaoxuan Zheng
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Zijian Ni
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Quanbing Pei
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Mengmeng Wang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Junjun Tan
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Shiyu Bai
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Fangwen Shi
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Shuji Ye
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
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21
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Novikova OD, Rybinskaya TV, Zelepuga EA, Uversky VN, Kim NY, Chingizova EA, Menchinskaya ES, Khomenko VA, Chistyulin DK, Portnyagina OY. Formation of Amyloid-Like Conformational States of β-Structured Membrane Proteins on the Example of OMPF Porin from the Yersinia pseudotuberculosis Outer Membrane. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:1079-1093. [PMID: 38981702 DOI: 10.1134/s0006297924060087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/14/2024] [Accepted: 03/31/2024] [Indexed: 07/11/2024]
Abstract
The work presents results of the in vitro and in silico study of formation of amyloid-like structures under harsh denaturing conditions by non-specific OmpF porin of Yersinia pseudotuberculosis (YpOmpF), a membrane protein with β-barrel conformation. It has been shown that in order to obtain amyloid-like porin aggregates, preliminary destabilization of its structure in a buffer solution with acidic pH at elevated temperature followed by long-term incubation at room temperature is necessary. After heating at 95°C in a solution with pH 4.5, significant conformational rearrangements are observed in the porin molecule at the level of tertiary and secondary structure of the protein, which are accompanied by the increase in the content of total β-structure and sharp decrease in the value of characteristic viscosity of the protein solution. Subsequent long-term exposure of the resulting unstable intermediate YpOmpF at room temperature leads to formation of porin aggregates of various shapes and sizes that bind thioflavin T, a specific fluorescent dye for the detection of amyloid-like protein structures. Compared to the initial protein, early intermediates of the amyloidogenic porin pathway, oligomers, have been shown to have increased toxicity to the Neuro-2aCCL-131™ mouse neuroblastoma cells. The results of computer modeling and analysis of the changes in intrinsic fluorescence during protein aggregation suggest that during formation of amyloid-like aggregates, changes in the structure of YpOmpF affect not only the areas with an internally disordered structure corresponding to the external loops of the porin, but also main framework of the molecule, which has a rigid spatial structure inherent to β-barrel.
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Affiliation(s)
- Olga D Novikova
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690021, Russia
| | - Tatyana V Rybinskaya
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690021, Russia
| | - Elena A Zelepuga
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690021, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33620, USA
| | - Nataliya Yu Kim
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690021, Russia
| | - Ekaterina A Chingizova
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690021, Russia
| | - Ekaterina S Menchinskaya
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690021, Russia
| | - Valentina A Khomenko
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690021, Russia
| | - Dmitriy K Chistyulin
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690021, Russia
| | - Olga Yu Portnyagina
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690021, Russia.
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22
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Ock J, Mollaei P, Barati Farimani A. GradNav: Accelerated Exploration of Potential Energy Surfaces with Gradient-Based Navigation. J Chem Theory Comput 2024; 20:4088-4098. [PMID: 38728667 PMCID: PMC11137815 DOI: 10.1021/acs.jctc.4c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/12/2024]
Abstract
Exploring the potential energy surface (PES) of molecular systems is important for comprehending their complex behaviors, particularly through the identification of various metastable states. However, the transition between these states is often hindered by substantial energy barriers, demanding prolonged molecular simulations that consume considerable computational resources. Our study introduces the gradient-based navigation (GradNav) algorithm, which accelerates the exploration of the energy surface and enables proper reconstruction of the PES. This algorithm employs a strategy of initiating short simulation runs from updated starting points derived from prior observations to effectively navigate across potential barriers and explore new regions. To evaluate GradNav's performance, we introduce two metrics: the deepest well escape frame (DWEF) and the search success initialization ratio (SSIR). Through applications on Langevin dynamics within Müller-type PESs and molecular dynamics simulations of the Fs-peptide protein, these metrics demonstrate GradNav's enhanced ability to escape deep energy wells and its reduced reliance on initial conditions, as denoted by the reduced DWEF values and increased SSIR values, respectively. Consequently, this improved exploration capability enables more precise energy estimations from simulation trajectories.
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Affiliation(s)
- Janghoon Ock
- Department
of Chemical Engineering, Carnegie Mellon
University, 5000 Forbes Street, Pittsburgh, Pennsylvania 15213, United States
| | - Parisa Mollaei
- Department
of Mechanical Engineering, Carnegie Mellon
University, 5000 Forbes
Street, Pittsburgh, Pennsylvania 15213, United States
| | - Amir Barati Farimani
- Department
of Mechanical Engineering, Carnegie Mellon
University, 5000 Forbes
Street, Pittsburgh, Pennsylvania 15213, United States
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23
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Dolui S, Roy A, Pal U, Kundu S, Pandit E, N Ratha B, Pariary R, Saha A, Bhunia A, Maiti NC. Raman Spectroscopic Insights of Phase-Separated Insulin Aggregates. ACS PHYSICAL CHEMISTRY AU 2024; 4:268-280. [PMID: 38800728 PMCID: PMC11117687 DOI: 10.1021/acsphyschemau.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 05/29/2024]
Abstract
Phase-separated protein accumulation through the formation of several aggregate species is linked to the pathology of several human disorders and diseases. Our current investigation envisaged detailed Raman signature and structural intricacy of bovine insulin in its various forms of aggregates produced in situ at an elevated temperature (60 °C). The amide I band in the Raman spectrum of the protein in its native-like conformation appeared at 1655 cm-1 and indicated the presence of a high content of α-helical structure as prepared freshly in acidic pH. The disorder content (turn and coils) also was predominately present in both the monomeric and oligomeric states and was confirmed by the presence shoulder amide I maker band at ∼1680 cm-1. However, the band shifted to ∼1671 cm-1 upon the transformation of the protein solution into fibrillar aggregates as produced for a longer time of incubation. The protein, however, maintained most of its helical conformation in the oligomeric phase; the low-frequency backbone α-helical conformation signal at ∼935 cm-1 was similar to that of freshly prepared aqueous protein solution enriched in helical conformation. The peak intensity was significantly weak in the fibrillar aggregates, and it appeared as a good Raman signature to follow the phase separation and the aggregation behavior of insulin and similar other proteins. Tyrosine phenoxy moieties in the protein may maintained its H-bond donor-acceptor integrity throughout the course of fibril formation; however, it entered in more hydrophobic environment in its journey of fibril formation. In addition, it was noticed that oligomeric bovine insulin maintained the orientation/conformation of the disulfide bonds. However, in the fibrillar state, the disulfide linkages became more strained and preferred to maintain a single conformation state.
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Affiliation(s)
- Sandip Dolui
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Anupam Roy
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Uttam Pal
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Shubham Kundu
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Esha Pandit
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Bhisma N Ratha
- Department
of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake,
Sector V, Kolkata 700091, India
| | - Ranit Pariary
- Department
of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake,
Sector V, Kolkata 700091, India
| | - Achintya Saha
- Department
of Chemical Technology, University of Calcutta, 92 Acharya Prafulla Chandra Road, Calcutta 700009, India
| | - Anirban Bhunia
- Department
of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake,
Sector V, Kolkata 700091, India
| | - Nakul C. Maiti
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
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24
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Mukherjee S, Poudyal M, Dave K, Kadu P, Maji SK. Protein misfolding and amyloid nucleation through liquid-liquid phase separation. Chem Soc Rev 2024; 53:4976-5013. [PMID: 38597222 DOI: 10.1039/d3cs01065a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.
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Affiliation(s)
- Semanti Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manisha Poudyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Kritika Dave
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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25
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Yuan L, Sun H, Ma X, Wang Y, Guo Z, Qi X, Le S, Chen H. Ligand-dependent folding and unfolding dynamics and free energy landscapes of acylphosphatase. SOFT MATTER 2024; 20:3780-3786. [PMID: 38639061 DOI: 10.1039/d4sm00131a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Acylphosphatase (AcP) is an enzyme which catalyses the hydrolysis of acylphosphate. The binding with the phosphate ion (Pi) assumes significance in preserving both the stability and enzymatic activity of AcP. While previous studies using single molecule force spectroscopy explored the mechanical properties of AcP, the influence of Pi on its folding and unfolding dynamic behaviors remains unexplored. In this work, using stable magnetic tweezers, we measured and compared the force-dependent folding and unfolding rates of AcP in the Tris buffer and phosphate buffer within a force range from 2 pN to 40 pN. We found that Pi exerts no discernible effect on the folding dynamics but consistently decreases the force-dependent unfolding rate of AcP by a constant ratio across the entire force spectrum. The free energy landscapes of AcP in the absence and presence of Pi are constructed. Our results reveal that Pi selectively binds to the native state of AcP, stabilizing it and suggesting the general properties of specific ligand-receptor interactions.
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Affiliation(s)
- Li Yuan
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China.
| | - Hao Sun
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Xuening Ma
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China.
| | - Yang Wang
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Zilong Guo
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Xingyu Qi
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China.
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Shimin Le
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China.
| | - Hu Chen
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China.
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
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26
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Olgenblum GI, Hutcheson BO, Pielak GJ, Harries D. Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels. Chem Rev 2024; 124:5668-5694. [PMID: 38635951 PMCID: PMC11082905 DOI: 10.1021/acs.chemrev.3c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 04/20/2024]
Abstract
Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations.
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Affiliation(s)
- Gil I. Olgenblum
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| | - Brent O. Hutcheson
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
| | - Gary J. Pielak
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
- Department
of Chemistry, Department of Biochemistry & Biophysics, Integrated
Program for Biological & Genome Sciences, Lineberger Comprehensive
Cancer Center, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Daniel Harries
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
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27
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Gao L, Tang Z, Lin J, Cai C, Guerin G. Living Growth Kinetics of Polymeric Micelles on a Substrate. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:9613-9621. [PMID: 38656106 DOI: 10.1021/acs.langmuir.4c00395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Living growth of micelles on the substrate is an intriguing phenomenon; however, little is known about its growth kinetics, especially from a theoretical viewpoint. Here, we examine the living growth kinetics of polymeric micelles on a hydrophobic substrate immersed in an aqueous solution. The block copolymers first assemble into short cylinder seeds anchored on the substrate. Then, the small aggregates of block copolymers in the solutions fuse onto the active ends of the anchored seeds, leading to micelle growth on the substrate. A theoretical model is proposed to interpret such living growth kinetics. It is revealed that the growth rate coefficient on the substrate is independent of the copolymer concentration and the multistep feedings; however, it is significantly affected by the surface hydrophobicity. Brownian dynamics simulations further support the proposed growth mechanism and the kinetic model. This work enriches living assembly systems and provides guidance for fabricating bioinspired surface nanostructures.
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Affiliation(s)
- Liang Gao
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhengmin Tang
- Department of Laboratory Medicine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 311121, China
| | - Jiaping Lin
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chunhua Cai
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Gerald Guerin
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
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28
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Li Y, Yin D, Lee SY, Lv Y. Engineered polymer nanoparticles as artificial chaperones facilitating the selective refolding of denatured enzymes. Proc Natl Acad Sci U S A 2024; 121:e2403049121. [PMID: 38691587 PMCID: PMC11087784 DOI: 10.1073/pnas.2403049121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/28/2024] [Indexed: 05/03/2024] Open
Abstract
Molecular chaperones assist in protein refolding by selectively binding to proteins in their nonnative states. Despite progress in creating artificial chaperones, these designs often have a limited range of substrates they can work with. In this paper, we present molecularly imprinted flexible polymer nanoparticles (nanoMIPs) designed as customizable biomimetic chaperones. We used model proteins such as cytochrome c, laccase, and lipase to screen polymeric monomers and identify the most effective formulations, offering tunable charge and hydrophobic properties. Utilizing a dispersed phase imprinting approach, we employed magnetic beads modified with destabilized whole-protein as solid-phase templates. This process involves medium exchange facilitated by magnetic pulldowns, resulting in the synthesis of nanoMIPs featuring imprinted sites that effectively mimic chaperone cavities. These nanoMIPs were able to selectively refold denatured enzymes, achieving up to 86.7% recovery of their activity, significantly outperforming control samples. Mechanistic studies confirmed that nanoMIPs preferentially bind denatured rather than native enzymes, mimicking natural chaperone interactions. Multifaceted analyses support the functionality of nanoMIPs, which emulate the protective roles of chaperones by selectively engaging with denatured proteins to inhibit aggregation and facilitate refolding. This approach shows promise for widespread use in protein recovery within biocatalysis and biomedicine.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing100029, China
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea
| | - Deping Yin
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing100029, China
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea
- KAIST Institute for the BioCentury, KAIST Institute for AI, BioProcess Engineering Research Center, BioInformatics Research Center, and Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea
| | - Yongqin Lv
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing100029, China
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29
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Węgrzyn E, Mejdrová I, Müller FM, Nainytė M, Escobar L, Carell T. RNA-Templated Peptide Bond Formation Promotes L-Homochirality. Angew Chem Int Ed Engl 2024; 63:e202319235. [PMID: 38407532 DOI: 10.1002/anie.202319235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
The world in which we live is homochiral. The ribose units that form the backbone of DNA and RNA are all D-configured and the encoded amino acids that comprise the proteins of all living species feature an all-L-configuration at the α-carbon atoms. The homochirality of α-amino acids is essential for folding of the peptides into well-defined and functional 3D structures and the homochirality of D-ribose is crucial for helix formation and base-pairing. The question of why nature uses only encoded L-α-amino acids is not understood. Herein, we show that an RNA-peptide world, in which peptides grow on RNAs constructed from D-ribose, leads to the self-selection of homo-L-peptides, which provides a possible explanation for the homo-D-ribose and homo-L-amino acid combination seen in nature.
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Affiliation(s)
- Ewa Węgrzyn
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Ivana Mejdrová
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Felix M Müller
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Milda Nainytė
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Luis Escobar
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
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30
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Yu D, Luo Y, Guo R, Ma F, Chang Y, Dang J. Comprehensive profiling of endocrine metabolism identifies a novel signature with robust predictive value in ovarian cancer. J Gene Med 2024; 26:e3686. [PMID: 38689382 DOI: 10.1002/jgm.3686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 03/05/2024] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND The cell endocrine pathway is a critical physiological process composed of the endoplasmic reticulum, Golgi apparatus and associated vesicles. Loss of enzymes or proteins can cause dysfunction of endoplasmic reticulum and Golgi apparatus and affect secretion pathways leading to a variety of human diseases, including cancer. METHODS The single-cell RNA sequencing and single nucleotide variant principal component analysis data of ovarian cancer were retrieved from The Cancer Genome Atlas and Gene Expression Omnibus (GEO) datasets. Eighty-four genes from SECRETORY_PATHWAYs were obtained from the gene set enrichment analysis (GSEA) website. Univariate cox regression analyses and ConsensusClusterPlus were used to identify prognostic genes and molecular subtypes, which were validated using the tumor immune dysfunction and exclusion (i.e. TIDE) analysis and gene mutation analysis. A prognosis model was established by randomForestSRC. Abundant infiltrated immune cells and pathway enrichment analyses were carried out, respectively, through ssGSEA, ESTIMATE, MCP-counter and GSEA. The drug sensitive analysis was performed using pRRophetic package. Immunotherapy datasets and pan-carcinoma analysis were used to examine the performance of prognostic model. RESULTS Eighteen prognostic genes from SECRETORY_PATHWAYs were found in both TCGA and GEO datasets. Next, two clusters (C1 and C2) were determined, for which C1 with a poor prognosis had higher immune infiltration. Tumor-related pathways, such as PATHWAYS_IN_CANCER and B_CELL_RECEPTOR_SIGNALING_PATHWAY, were enriched in C1. Moreover, C2 was suitable for immunotherapy. A four-gene (DNAJA1, NDRG3, LUZP1 and ZCCHC24) signature was developed and successfully validated. RiskScore of higher levels were significantly associated with worse prognoses. An enhanced immune infiltration, increased pathways score and inappropriate immunotherapy were observed in the high RiskScore group. The high- and low-RiskScore groups had different drug sensitivities. Immunotherapy datasets and pan-carcinoma analysis indicated that the low RiskScore group may benefit from immunotherapy. CONCLUSIONS Based on the perspective of the secretory signaling pathway, a robust prognostic signature with great performances was determined, which may provide clues for clinical precision treatment of ovarian cancer.
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Affiliation(s)
- Dan Yu
- Department of General Medicine, Changzheng Hospital, The Naval Military Medical University, Shanghai, China
| | - Yan Luo
- Department of Obstetrics and Gynecology, Nanjing Yimin Hospital, Nanjing, China
| | - Rong Guo
- Department of General Medicine, Changzheng Hospital, The Naval Military Medical University, Shanghai, China
| | - Fang Ma
- Department of Obstetrics and Gynecology, Changzheng Hospital, The Naval Military Medical University, Shanghai, China
| | - Yunyun Chang
- Department of General Medicine, Changzheng Hospital, The Naval Military Medical University, Shanghai, China
| | - Jianhong Dang
- Department of Obstetrics and Gynecology, Changzheng Hospital, The Naval Military Medical University, Shanghai, China
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31
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Khorsand FR, Aziziyan F, Khajeh K. Factors influencing amyloid fibril formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:55-83. [PMID: 38811089 DOI: 10.1016/bs.pmbts.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Protein aggregation is a complex process with several stages that lead to the formation of complex structures and shapes with a broad variability in stability and toxicity. The aggregation process is affected by various factors and environmental conditions that disrupt the protein's original state, including internal factors like mutations, expression levels, and polypeptide chain truncation, as well as external factors, such as dense molecular surroundings, post-translation modifications, and interactions with other proteins, nucleic acids, small molecules, metal ions, chaperones, and lipid membranes. During the aggregation process, the biological activity of an aggregating protein may be reduced or eliminated, whereas the resulting aggregates may have the potential to be immunogenic, or they may have other undesirable properties. Finding the cause(s) of protein aggregation and controlling it to an acceptable level is among the most crucial topics of research in academia and biopharmaceutical companies. This chapter aims to review intrinsic pathways of protein aggregation and potential extrinsic variables that influence this process.
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Affiliation(s)
| | - Fatemeh Aziziyan
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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32
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Thiel A, Speranza MJ, Jadhav S, Stevens LL, Unruh DK, Ren P, Ponder JW, Shen J, Schnieders MJ. Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. J Chem Theory Comput 2024; 20:2921-2933. [PMID: 38507252 PMCID: PMC11008096 DOI: 10.1021/acs.jctc.3c01180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024]
Abstract
Accurately predicting protein behavior across diverse pH environments remains a significant challenge in biomolecular simulations. Existing constant-pH molecular dynamics (CpHMD) algorithms are limited to fixed-charge force fields, hindering their application to biomolecular systems described by permanent atomic multipoles or induced dipoles. This work overcomes these limitations by introducing the first polarizable CpHMD algorithm in the context of the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. Additionally, our implementation in the open-source Force Field X (FFX) software has the unique ability to handle titration state changes for crystalline systems including flexible support for all 230 space groups. The evaluation of constant-pH molecular dynamics (CpHMD) with the AMOEBA force field was performed on 11 crystalline peptide systems that span the titrating amino acids (Asp, Glu, His, Lys, and Cys). Titration states were correctly predicted for 15 out of the 16 amino acids present in the 11 systems, including for the coordination of Zn2+ by cysteines. The lone exception was for a HIS-ALA peptide where CpHMD predicted both neutral histidine tautomers to be equally populated, whereas the experimental model did not consider multiple conformers and diffraction data are unavailable for rerefinement. This work demonstrates the promise polarizable CpHMD simulations for pKa predictions, the study of biochemical mechanisms such as the catalytic triad of proteases, and for improved protein-ligand binding affinity accuracy in the context of pharmaceutical lead optimization.
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Affiliation(s)
- Andrew
C. Thiel
- Department
of Biomedical Engineering, University of
Iowa, Iowa City, Iowa 52242, United States
| | - Matthew J. Speranza
- Department
of Biomedical Engineering, University of
Iowa, Iowa City, Iowa 52242, United States
| | - Sanika Jadhav
- Department
of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Lewis L. Stevens
- Department
of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Daniel K. Unruh
- Office
of the Vice President for Research, University
of Iowa, Iowa City, Iowa 52242, United
States
| | - Pengyu Ren
- Department
of Biomedical Engineering, University of
Texas, Austin, Texas 78712, United States
| | - Jay W. Ponder
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United
States
| | - Jana Shen
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Michael J. Schnieders
- Department
of Biomedical Engineering, University of
Iowa, Iowa City, Iowa 52242, United States
- Department
of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
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33
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Galvagnion C, Barclay A, Makasewicz K, Marlet FR, Moulin M, Devos JM, Linse S, Martel A, Porcar L, Sparr E, Pedersen MC, Roosen-Runge F, Arleth L, Buell AK. Structural characterisation of α-synuclein-membrane interactions and the resulting aggregation using small angle scattering. Phys Chem Chem Phys 2024; 26:10998-11013. [PMID: 38526443 DOI: 10.1039/d3cp05928f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
The presence of amyloid fibrils is a hallmark of several neurodegenerative diseases. Some amyloidogenic proteins, such as α-synuclein and amyloid β, interact with lipids, and this interaction can strongly favour the formation of amyloid fibrils. In particular the primary nucleation step, i.e. the de novo formation of amyloid fibrils, has been shown to be accelerated by lipids. However, the exact mechanism of this acceleration is still mostly unclear. Here we use a range of scattering methods, such as dynamic light scattering (DLS) and small angle X-ray and neutron scattering (SAXS and SANS) to obtain structural information on the binding of α-synuclein to model membranes formed from negatively charged lipids and their co-assembly into amyloid fibrils. We find that the model membranes take an active role in the reaction. The binding of α synuclein to the model membranes immediately induces a major structural change in the lipid assembly, which leads to a break-up into small and mostly disc- or rod-like lipid-protein particles. This transition can be reversed by temperature changes or proteolytic protein removal. Incubation of the small lipid-α-synuclein particles for several hours, however, leads to amyloid fibril formation, whereby the lipids are incorporated into the amyloid fibrils.
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Affiliation(s)
- Céline Galvagnion
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Abigail Barclay
- Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Katarzyna Makasewicz
- Division of Physical Chemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| | | | - Martine Moulin
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Juliette M Devos
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, SE22100 Lund, Sweden
| | - Anne Martel
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Lionel Porcar
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Emma Sparr
- Division of Physical Chemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| | | | - Felix Roosen-Runge
- Division of Physical Chemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
- Department of Biomedical Sciences and Biofilms Research Center for Biointerfaces, Malmö University, Malmö, Sweden
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
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34
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Bashir S, Aiman A, Shahid M, Chaudhary AA, Sami N, Basir SF, Hassan I, Islam A. Amyloid-induced neurodegeneration: A comprehensive review through aggregomics perception of proteins in health and pathology. Ageing Res Rev 2024; 96:102276. [PMID: 38499161 DOI: 10.1016/j.arr.2024.102276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
Amyloidosis of protein caused by fibrillation and aggregation are some of the most exciting new edges not only in protein sciences but also in molecular medicines. The present review discusses recent advancements in the field of neurodegenerative diseases and therapeutic applications with ongoing clinical trials, featuring new areas of protein misfolding resulting in aggregation. The endogenous accretion of protein fibrils having fibrillar morphology symbolizes the beginning of neuro-disorders. Prognostic amyloidosis is prominent in numerous degenerative infections such as Alzheimer's and Parkinson's disease, Amyotrophic lateral sclerosis (ALS), etc. However, the molecular basis determining the intracellular or extracellular evidence of aggregates, playing a significant role as a causative factor in neurodegeneration is still unclear. Structural conversions and protein self-assembly resulting in the formation of amyloid oligomers and fibrils are important events in the pathophysiology of the disease. This comprehensive review sheds light on the evolving landscape of potential treatment modalities, highlighting the ongoing clinical trials and the potential socio-economic impact of novel therapeutic interventions in the realm of neurodegenerative diseases. Furthermore, many drugs are undergoing different levels of clinical trials that would certainly help in treating these disorders and will surely improve the socio-impact of human life.
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Affiliation(s)
- Sania Bashir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Ayesha Aiman
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia.
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia.
| | - Neha Sami
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Seemi Farhat Basir
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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35
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Rose M, Manikandan SK. Role of interactions in nonequilibrium transformations. Phys Rev E 2024; 109:044136. [PMID: 38755940 DOI: 10.1103/physreve.109.044136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/28/2024] [Indexed: 05/18/2024]
Abstract
For arbitrary nonequilibrium transformations in complex systems, we show that the distance between the current state and a target state can be decomposed into two terms: one corresponding to an independent estimate of the distance, and another corresponding to interactions, quantified using the relative mutual information between the variables. This decomposition is a special case of a more general decomposition involving successive orders of correlation or interactions among the degrees of freedom of the system. To illustrate its practical significance, we study the thermal relaxation of two interacting, optically trapped colloidal particles, where increasing pairwise interaction strength is shown to prolong the longevity of the time-dependent nonequilibrium state. Additionally, we study a system with both pairwise and triplet interactions, where our approach identifies their distinct contributions to the transformation. In more general setups where it is possible to control the strength of different orders of interactions, our findings provide a way to disentangle their effects and identify interactions that facilitate the transformation.
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Affiliation(s)
- Maria Rose
- School of Pure and Applied Physics, Mahatma Gandhi University, 686560 Kottayam, India
| | - Sreekanth K Manikandan
- NORDITA, KTH Royal Institute of Technology and Stockholm University, Roslagstullsbacken 23, 10691 Stockholm, Sweden and Department of Chemistry, Stanford University, Stanford, California 94305, USA
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36
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Marino V, Phromkrasae W, Bertacchi M, Cassini P, Chakrabandhu K, Dell'Orco D, Studer M. Disrupted protein interaction dynamics in a genetic neurodevelopmental disorder revealed by structural bioinformatics and genetic code expansion. Protein Sci 2024; 33:e4953. [PMID: 38511490 PMCID: PMC10955615 DOI: 10.1002/pro.4953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 03/22/2024]
Abstract
Deciphering the structural effects of gene variants is essential for understanding the pathophysiological mechanisms of genetic diseases. Using a neurodevelopmental disorder called Bosch-Boonstra-Schaaf Optic Atrophy Syndrome (BBSOAS) as a genetic disease model, we applied structural bioinformatics and Genetic Code Expansion (GCE) strategies to assess the pathogenic impact of human NR2F1 variants and their binding with known and novel partners. While the computational analyses of the NR2F1 structure delineated the molecular basis of the impact of several variants on the isolated and complexed structures, the GCE enabled covalent and site-specific capture of transient supramolecular interactions in living cells. This revealed the variable quaternary conformations of NR2F1 variants and highlighted the disrupted interplay with dimeric partners and the newly identified co-factor, CRABP2. The disclosed consequence of the pathogenic mutations on the conformation, supramolecular interplay, and alterations in the cell cycle, viability, and sub-cellular localization of the different variants reflect the heterogeneous disease spectrum of BBSOAS and set up novel foundation for unveiling the complexity of neurodevelopmental diseases.
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Affiliation(s)
- Valerio Marino
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological ChemistryUniversity of VeronaVeronaItaly
| | | | | | - Paul Cassini
- University Côte d'Azur, CNRS, Inserm, iBVNiceFrance
| | | | - Daniele Dell'Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological ChemistryUniversity of VeronaVeronaItaly
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37
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Shahsavani MB, Hoshino M, Kumar A, Yousefi R. Charge manipulation of the human insulin B chain C-terminal to shed light on the complex mechanism of insulin fibrillation. Biochim Biophys Acta Gen Subj 2024; 1868:130578. [PMID: 38278307 DOI: 10.1016/j.bbagen.2024.130578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/13/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Insulin fibrillation poses a significant challenge in the development and treatment of diabetes. Current efforts to unravel its mechanisms have thus far remained incomplete. To shed light on the intricate processes behind insulin fibrillation, we employed mutagenesis techniques to introduce additional positive charge residues into the C-terminal region of the insulin B chain which plays an important role in insulin dimerization. We employed our investigation with various spectroscopic methods, electron microscopy, and molecular dynamics simulations. These methods allowed us to explore the structure and fibrillation behavior of the engineered B chains following their expression in a bacterial host and successful purification. This manipulation had a pronounced impact on the oligomerization behavior of the insulin B chain. It appears that these mutations delay the formation of the dimeric state in the process of transitioning to larger oligomers, consequently, leading to an alteration in the kinetics of fibrillation. Our findings also indicated that the mutant insulin B chains (Di-R, Di-K, and Di-H) displayed resistance to the initiation of fibrillation. This resistance can be attributed to the repulsive forces generated by the introduced positive charges, which disrupt the attractive interactions favoring nucleation. Notably, the mutant B chains formed shorter and less abundant oligomers and fibrils, which can be ascribed to the alterations induced by repulsion. Our engineered mutant B chains exhibited enhanced stability against stress-induced fibrillation, hinting at their potential utility in the development of new insulin analogs. This study underscores the significance of the C-terminal region in the initial stages of insulin B chain fibrillation, providing valuable insights into the intricate mechanisms involved and their potential pharmaceutical applications.
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Affiliation(s)
- Mohammad Bagher Shahsavani
- Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Masaru Hoshino
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Reza Yousefi
- Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran; Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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38
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Murthy MK, Khandayataray P, Mohanty CS, Pattanayak R. Investigating the toxic mechanism of iron oxide nanoparticles-induced oxidative stress in tadpole (Duttaphrynus melanostictus): A combined biochemical and molecular study. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2024; 107:104432. [PMID: 38554986 DOI: 10.1016/j.etap.2024.104432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/09/2023] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Metal oxide nanomaterials have toxicity towards aquatic organisms, especially microbes and invertebrates, but little is known about their impact on amphibians. We conducted a study on Duttaphrynus melanostictus (D. melanostictus) tadpoles to explore the chronic toxicity effects of iron oxide nanoparticles (IONPs) and the underlying mechanisms of IONPs-induced oxidative stress. IONPs exposure led to increased iron accumulation in the blood, liver, and kidneys of tadpoles, significantly affecting blood parameters and morphology. Higher IONPs concentrations (10 and 50 mg L-1) triggered reactive oxygen species generation, resulting in lipid peroxidation, oxidative stress, and pronounced toxicity in tadpoles. The activity levels of antioxidant enzymes/proteins (SOD, CAT, albumin, and lysozyme) decreased after IONPs exposure, and immunological measures in the blood serum were significantly reduced compared to the control group. Molecular docking analysis revealed that IONPs primarily attached to the surface of SOD/CAT/albumin/lysozyme through hydrogen bonding and hydrophobic forces. Overall, this study emphasizes the ability of IONPs to induce oxidative damage by decreasing immunological profiles such as ACH50 (34.58 ± 2.74 U mL-1), lysozyme (6.94 ± 0.82 U mL-1), total Ig (5.00 ± 0.35 g dL-1), total protein (1.20 ± 0.17 g dL-1), albumin (0.52 ± 0.01 g dL-1) and globulin (0.96 ± 0.01 g dL-1) and sheds light on their potential toxic effects on tadpoles.
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Affiliation(s)
- Meesala Krishna Murthy
- Department of Allied Health Sciences, Chitkara School of Health Sciences, Chitkara University, Punjab 140401, India; Department of Zoology, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha 751003, India
| | - Pratima Khandayataray
- Department of Biotechnology, Academy of Management and Information Technology, Utkal University, Bhubaneswar, Odisha 752057, India
| | - Chandra Sekhar Mohanty
- Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh 226001, India
| | - Rojalin Pattanayak
- Department of Zoology, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha 751003, India.
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39
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Servín Muñoz IV, Ortuño-Sahagún D, Griñán-Ferré C, Pallàs M, González-Castillo C. Alterations in Proteostasis Mechanisms in Niemann-Pick Type C Disease. Int J Mol Sci 2024; 25:3806. [PMID: 38612616 PMCID: PMC11011983 DOI: 10.3390/ijms25073806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 04/14/2024] Open
Abstract
Niemann-Pick Type C (NPC) represents an autosomal recessive disorder with an incidence rate of 1 in 150,000 live births, classified within lysosomal storage diseases (LSDs). The abnormal accumulation of unesterified cholesterol characterizes the pathophysiology of NPC. This phenomenon is not unique to NPC, as analogous accumulations have also been observed in Alzheimer's disease, Parkinson's disease, and other neurodegenerative disorders. Interestingly, disturbances in the folding of the mutant protein NPC1 I1061T are accompanied by the aggregation of proteins such as hyperphosphorylated tau, α-synuclein, TDP-43, and β-amyloid peptide. These accumulations suggest potential disruptions in proteostasis, a regulatory process encompassing four principal mechanisms: synthesis, folding, maintenance of folding, and protein degradation. The dysregulation of these processes leads to excessive accumulation of abnormal proteins that impair cell function and trigger cytotoxicity. This comprehensive review delineates reported alterations across proteostasis mechanisms in NPC, encompassing changes in processes from synthesis to degradation. Additionally, it discusses therapeutic interventions targeting pharmacological facets of proteostasis in NPC. Noteworthy among these interventions is valproic acid, a histone deacetylase inhibitor (HDACi) that modulates acetylation during NPC1 synthesis. In addition, various therapeutic options addressing protein folding modulation, such as abiraterone acetate, DHBP, calnexin, and arimoclomol, are examined. Additionally, treatments impeding NPC1 degradation, exemplified by bortezomib and MG132, are explored as potential strategies. This review consolidates current knowledge on proteostasis dysregulation in NPC and underscores the therapeutic landscape targeting diverse facets of this intricate process.
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Affiliation(s)
- Iris Valeria Servín Muñoz
- Laboratorio de Neuroinmunobiología Molecular, Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - Daniel Ortuño-Sahagún
- Laboratorio de Neuroinmunobiología Molecular, Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara 44340, Mexico;
| | - Christian Griñán-Ferré
- Pharmacology Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, Universitat de Barcelona, 08028 Barcelona, Spain; (C.G.-F.); (M.P.)
- Centro de Investigación Biomédica en Red (CiberNed), Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28220 Madrid, Spain
| | - Mercè Pallàs
- Pharmacology Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, Universitat de Barcelona, 08028 Barcelona, Spain; (C.G.-F.); (M.P.)
- Centro de Investigación Biomédica en Red (CiberNed), Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28220 Madrid, Spain
| | - Celia González-Castillo
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Campus Guadalajara, Zapopan 45201, Mexico
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40
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Yuan J, Tanaka H. Impact of Hydrodynamic Interactions on the Kinetic Pathway of Protein Folding. PHYSICAL REVIEW LETTERS 2024; 132:138402. [PMID: 38613272 DOI: 10.1103/physrevlett.132.138402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 02/29/2024] [Indexed: 04/14/2024]
Abstract
Protein folding is a fundamental process critical to cellular function and human health, but it remains a grand challenge in biophysics. Hydrodynamic interaction (HI) plays a vital role in the self-organization of soft and biological materials, yet its role in protein folding is not fully understood despite folding occurring in a fluid environment. Here, we use the fluid particle dynamics method to investigate many-body hydrodynamic couplings between amino acid residues and fluid motion in the folding kinetics of a coarse-grained four-α-helices bundle protein. Our results reveal that HI helps select fast folding pathways to the native state without being kinetically trapped, significantly speeding up the folding kinetics compared to its absence. First, the directional flow along the protein backbone expedites protein collapse. Then, the incompressibility-induced squeezing flow effects retard the accumulation of non-native hydrophobic contacts, thus preventing the protein from being trapped in local energy minima during the conformational search of the native structure. We also find that the significance of HI in folding kinetics depends on temperature, with a pronounced effect under biologically relevant conditions. Our findings suggest that HI, particularly the short-range squeezing effect, may be crucial in avoiding protein misfolding.
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Affiliation(s)
- Jiaxing Yuan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hajime Tanaka
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Fundamental Engineering, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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41
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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42
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Chen S, Puri A, Bell B, Fritsche J, Palacios HH, Balch M, Sprunger ML, Howard MK, Ryan JJ, Haines JN, Patti GJ, Davis AA, Jackrel ME. HTRA1 disaggregates α-synuclein amyloid fibrils and converts them into non-toxic and seeding incompetent species. Nat Commun 2024; 15:2436. [PMID: 38499535 PMCID: PMC10948756 DOI: 10.1038/s41467-024-46538-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/01/2024] [Indexed: 03/20/2024] Open
Abstract
Parkinson's disease (PD) is closely linked to α-synuclein (α-syn) misfolding and accumulation in Lewy bodies. The PDZ serine protease HTRA1 degrades fibrillar tau, which is associated with Alzheimer's disease, and inactivating mutations to mitochondrial HTRA2 are implicated in PD. Here, we report that HTRA1 inhibits aggregation of α-syn as well as FUS and TDP-43, which are implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. The protease domain of HTRA1 is necessary and sufficient for inhibiting aggregation, yet this activity is proteolytically-independent. Further, HTRA1 disaggregates preformed α-syn fibrils, rendering them incapable of seeding aggregation of endogenous α-syn, while reducing HTRA1 expression promotes α-syn seeding. HTRA1 remodels α-syn fibrils by targeting the NAC domain, the key domain catalyzing α-syn amyloidogenesis. Finally, HTRA1 detoxifies α-syn fibrils and prevents formation of hyperphosphorylated α-syn accumulations in primary neurons. Our findings suggest that HTRA1 may be a therapeutic target for a range of neurodegenerative disorders.
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Affiliation(s)
- Sheng Chen
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Anuradhika Puri
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Braxton Bell
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Joseph Fritsche
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Hector H Palacios
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Maurie Balch
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Macy L Sprunger
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Matthew K Howard
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Jeremy J Ryan
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Jessica N Haines
- Department of Neurology, Washington University, St. Louis, MO, 63130, USA
| | - Gary J Patti
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
- Department of Medicine, Washington University, St. Louis, MO, 63130, USA
| | - Albert A Davis
- Department of Neurology, Washington University, St. Louis, MO, 63130, USA
| | - Meredith E Jackrel
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA.
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43
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Plett C, Grimme S, Hansen A. Conformational energies of biomolecules in solution: Extending the MPCONF196 benchmark with explicit water molecules. J Comput Chem 2024; 45:419-429. [PMID: 37982322 DOI: 10.1002/jcc.27248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/21/2023]
Abstract
A prerequisite for the computational prediction of molecular properties like conformational energies of biomolecules is a reliable, robust, and computationally affordable method usually selected according to its performance for relevant benchmark sets. However, most of these sets comprise molecules in the gas phase and do not cover interactions with a solvent, even though biomolecules typically occur in aqueous solution. To address this issue, we introduce a with explicit water molecules solvated version of a gas-phase benchmark set containing 196 conformers of 13 peptides and other relevant macrocycles, namely MPCONF196 [J. Řezáč et al., JCTC 2018, 14, 1254-1266], and provide very accurate PNO-LCCSD(T)-F12b/AVQZ' reference values. The novel solvMPCONF196 benchmark set features two additional challenges beyond the description of conformers in the gas phase: conformer-water and water-water interactions. The overall best performing method for this set is the double hybrid revDSDPBEP86-D4/def2-QZVPP yielding conformational energies of almost coupled cluster quality. Furthermore, some (meta-)GGAs and hybrid functionals like B97M-V and ω B97M-D with a large basis set reproduce the coupled cluster reference with an MAD below 1 kcal mol- 1 . If more efficient methods are required, the composite DFT-method r2 SCAN-3c (MAD of 1.2 kcal mol- 1 ) is a good alternative, and when conformational energies of polypeptides or macrocycles with more than 500-1000 atoms are in the focus, the semi-empirical GFN2-xTB or the MMFF94 force field (for very large systems) are recommended.
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Affiliation(s)
- Christoph Plett
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Universität Bonn, Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Universität Bonn, Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Universität Bonn, Bonn, Germany
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44
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Shi Y, Sun Y, Li C, Wang S, Wang J, Shi H. Edge Substitution Effects of Histidine Tautomerization Behaviors on the Structural Properties and Aggregation Properties of Aβ(1-42) Mature Fibril. ACS Chem Neurosci 2024; 15:1055-1062. [PMID: 38379141 DOI: 10.1021/acschemneuro.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Histidine behaviors play critical roles in folding and misfolding processes due to the changes in net charge and the various N/N-H orientations on imidazole rings. However, the effect of histidine tautomerization (HIE (Nε-H, ε) and HID (Nδ-H, δ) states) behaviors on the edge chain of Aβ mature fibrils remains inadequately understood, which is critical for finding a strategy to disturb fibril elongation and growth. In the current study, eight independent molecular dynamics simulations were conducted to investigate such impacts on the structural and aggregation properties. Our results from three different binding models revealed that the binding contributions of edge substitution effects are primarily located between chains 1 and 2. Histidine states significantly influence the secondary structure of each domain. Further analysis confirmed that the C1_H6//C1_E11 intrachain interaction is essential in maintaining the internal stability of chain 1, while the C1_H13//C2_H13 and C1_H14//C2_H13 interchain interactions are critical in maintaining the interchain stability of the fibril structure. Our subsequent analysis revealed that the current edge substitution leads to the loss of the C1_H13//C1_E11 intrachain and C1_H13//C2_H14 interchain interactions. The N-terminal regularity was significantly directly influenced by histidine states, particularly by the residue of C1_H13. Our study provides valuable insights into the effect of histidine behaviors on the edge chain of Aβ mature fibril, advancing our understanding of the histidine behavior hypothesis in misfolding diseases.
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Affiliation(s)
- Yaru Shi
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Yue Sun
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Changgui Li
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Shuo Wang
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Jinping Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan 250022, Shandong, China
| | - Hu Shi
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
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45
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Jing B, Bi Y, Kong H, Wan W, Wang J, Yu B. Dual-environment-sensitive probe to detect protein aggregation in stressed laryngeal carcinoma cells and tissues. J Mater Chem B 2024; 12:2505-2510. [PMID: 38334693 DOI: 10.1039/d3tb02627b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
The interplay between protein folding and biological activity is crucial, with the integrity of the proteome being paramount to ensuring effective biological function execution. In this study, we report a dual-environment-sensitive probe A1, capable of selectively binding to protein aggregates and dynamically monitoring their formation and degradation. Through in vitro, cellular, and tissue assays, A1 demonstrated specificity in distinguishing aggregated from folded protein states, selectively partitioning into aggregated proteins. Thermal shift assays revealed A1 could monitor the process of protein aggregation upon binding to misfolded proteins and preceding to insoluble aggregate formation. In cellular models, A1 detected stress-induced proteome aggregation in TU212 cells (laryngeal carcinoma cells), revealing a less polar microenvironment within the aggregated proteome. Similarly, tissue samples showed more severe proteome aggregation in cancerous tissues compared to paracancerous tissues. Overall, A1 represents a versatile tool for probing protein aggregation with significant implications for both fundamental research and clinical diagnostics.
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Affiliation(s)
- Biao Jing
- Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yanjie Bi
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Hui Kong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Wang Wan
- Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Jizhe Wang
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Bo Yu
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
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46
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Brunzell E, Sigfridsson K, Gedda L, Edwards K, Bergström LM. Investigation of supramolecular structures in various aqueous solutions of an amyloid forming peptide using small-angle X-ray scattering. SOFT MATTER 2024; 20:2272-2279. [PMID: 38353286 DOI: 10.1039/d3sm01172k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Aggregation of peptide molecules into amyloid fibrils is a characteristic feature of several degenerative diseases. However, the details behind amyloid-formation, and other self-assembled peptide aggregates, remain poorly understood. In this study, we have used small-angle X-ray scattering (SAXS), static and dynamic light scattering (SLS and DLS) as well as cryogenic transmission electron microscopy (cryo-TEM) to determine the structural geometry of self-assembled peptide aggregates in various dilute aqueous solutions. Pramlintide was used as a model peptide to assess the aggregation behaviour of an amyloid-forming peptide. The effects of adding sodium chloride (NaCl), sodium thiocyanate (NaSCN), and sodium fluoride (NaF) and the co-solvent dimethyl sulfoxide (DMSO) on the aggregation behaviour were studied. Our scattering data analysis demonstrates that small oligomeric fibrils aggregate to form networks of supramolecular assemblies with fractal dimensions. The choice of anion in small amounts of added salt has a significant impact on the size of the fibrils as well as on the fractal dimensions of supramolecular clusters. In DMSO the fractal dimension decreased with increasing DMSO concentration, indicating the formation of a less compact structure of the supramolecular assemblies.
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Affiliation(s)
- Ellen Brunzell
- Department of Medicinal Chemistry, Pharmaceutical Physical Chemistry, Uppsala University, Uppsala 751 23, Sweden.
| | - Kalle Sigfridsson
- Advanced Drug Delivery, Pharmaceutical Science, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Lars Gedda
- Department of Chemistry-Ångström, Uppsala University, P.O. Box 573, Uppsala 751 23, Sweden
| | - Katarina Edwards
- Department of Chemistry-Ångström, Uppsala University, P.O. Box 573, Uppsala 751 23, Sweden
| | - L Magnus Bergström
- Department of Medicinal Chemistry, Pharmaceutical Physical Chemistry, Uppsala University, Uppsala 751 23, Sweden.
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47
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Stief T, Vormann K, Lakomek NA. Sensitivity-enhanced NMR 15N R 1 and R 1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields. Methods 2024; 223:1-15. [PMID: 38242384 DOI: 10.1016/j.ymeth.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/21/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024] Open
Abstract
NMR relaxation experiments provide residue-specific insights into the structural dynamics of proteins. Here, we present an optimized set of sensitivity-enhanced 15N R1 and R1ρ relaxation experiments applicable to fully protonated proteins. The NMR pulse sequences are conceptually similar to the set of TROSY-based sequences and their HSQC counterpart (Lakomek et al., J. Biomol. NMR 2012). Instead of the TROSY read-out scheme, a sensitivity-enhanced HSQC read-out scheme is used, with improved and easier optimized water suppression. The presented pulse sequences are applied on the cytoplasmic domain of the SNARE protein Synpatobrevin-2 (Syb-2), which is intrinsically disordered in its monomeric pre-fusion state. A two-fold increase in the obtained signal-to-noise ratio is observed for this intrinsically disordered protein, therefore offering a four-fold reduction of measurement time compared to the TROSY-detected version. The inter-scan recovery delay can be shortened to two seconds. Pulse sequences were tested at 600 MHz and 1200 MHz 1H Larmor frequency, thus applicable over a wide magnetic field range. A comparison between protonated and deuterated protein samples reveals high agreement, indicating that reliable 15N R1 and R1ρ rate constants can be extracted for fully protonated and deuterated samples. The presented pulse sequences will benefit not only for IDPs but also for an entire range of low and medium-sized proteins.
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Affiliation(s)
- Tobias Stief
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, Jülich, Germany; Institute of Physical Biology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Katharina Vormann
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, Jülich, Germany; Institute of Physical Biology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nils-Alexander Lakomek
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, Jülich, Germany; Institute of Physical Biology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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48
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Zhang D, Zhang J, Ma Z, Wu Q, Liu M, Fan T, Ding L, Ren D, Wen A, Wang J. Luteoloside inhibits Aβ1-42 fibrillogenesis, disintegrates preformed fibrils, and alleviates amyloid-induced cytotoxicity. Biophys Chem 2024; 306:107171. [PMID: 38194817 DOI: 10.1016/j.bpc.2023.107171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/17/2023] [Accepted: 12/30/2023] [Indexed: 01/11/2024]
Abstract
Abnormal aggregation and fibrillogenesis of amyloid-β protein (Aβ) can cause Alzheimer's disease (AD). Thus, the discovery of effective drugs that inhibit Aβ fibrillogenesis in the brain is crucial for the treatment of AD. Luteoloside, as one of the polyphenolic compounds, is found to have a certain therapeutic effect on nervous system diseases. However, it remains unknown whether luteoloside is a potential drug for treating AD by modulating Aβ aggregation pathway. In this study, we performed diverse biophysical and biochemical methods to explore the inhibition of luteoloside on Aβ1-42 which is linked to AD. The results demonstrated that luteoloside efficiently prevented amyloid oligomerization and cross-β-sheet formation, reduced the rate of amyloid growth and the length of amyloid fibrils in a dose-dependent manner. Moreover, luteoloside was able to influence aggregation and conformation of Aβ1-42 during different fiber-forming phases, and it could disintegrate already preformed fibrils of Aβ1-42 and convert them into nontoxic aggregates. Furthermore, luteoloside protected cells from amyloid-induced cytotoxicity and hemolysis, and attenuated the level of reactive oxygen species (ROS). The molecular docking study showed that luteoloside interacted with Aβ1-42 mainly via Conventional Hydrogen Bond, Carbon Hydrogen Bond, Pi-Pi T-shaped, Pi-Alkyl and Pi-Anion, thereby possibly preventing it from forming the aggregates. These observations indicate that luteoloside, a natural anti-oxidant molecule, may be applicable as an effective inhibitor of Aβ, and promote further exploration of the therapeutic strategy against AD.
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Affiliation(s)
- Di Zhang
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Juanli Zhang
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Zhongying Ma
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Qianwen Wu
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Meiyou Liu
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Tingting Fan
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Likun Ding
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Danjun Ren
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Aidong Wen
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China.
| | - Jingwen Wang
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China.
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49
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Roberts BS, Mitra D, Abishek S, Beher R, Satpute-Krishnan P. The p24-family and COPII subunit SEC24C facilitate the clearance of alpha1-antitrypsin Z from the endoplasmic reticulum to lysosomes. Mol Biol Cell 2024; 35:ar45. [PMID: 38294851 PMCID: PMC10916869 DOI: 10.1091/mbc.e23-06-0257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/01/2024] Open
Abstract
A subpopulation of the alpha-1-antitrypsin misfolding Z mutant (ATZ) is cleared from the endoplasmic reticulum (ER) via an ER-to-lysosome-associated degradation (ERLAD) pathway. Here, we report that the COPII subunit SEC24C and the p24-family of proteins facilitate the clearance of ATZ via ERLAD. In addition to the previously reported ERLAD components calnexin and FAM134B, we discovered that ATZ coimmunoprecipitates with the p24-family members TMP21 and TMED9. This contrasts with wild type alpha1-antitrypsin, which did not coimmunoprecipitate with FAM134B, calnexin or the p24-family members. Live-cell imaging revealed that ATZ and the p24-family members traffic together from the ER to lysosomes. Using chemical inhibitors to block ER exit or autophagy, we demonstrated that p24-family members and ATZ co-accumulate at SEC24C marked ER-exit sites or in ER-derived compartments, respectively. Furthermore, depletion of SEC24C, TMP21, or TMED9 inhibited lysosomal trafficking of ATZ and resulted in the increase of intracellular ATZ levels. Conversely, overexpression of these p24-family members resulted in the reduction of ATZ levels. Intriguingly, the p24-family members coimmunoprecipitate with ATZ, FAM134B, and SEC24C. Thus, we propose a model in which the p24-family functions in an adaptor complex linking SEC24C with the ERLAD machinery for the clearance of ATZ.
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Affiliation(s)
| | - Debashree Mitra
- Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Sudhanshu Abishek
- Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Richa Beher
- Uniformed Services University of the Health Sciences, Bethesda, MD 20814
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50
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Li ST, Hirayama H, Huang C, Matsuda T, Oka R, Yamasaki T, Kohda D, Suzuki T. Hydrolytic activity of yeast oligosaccharyltransferase is enhanced when misfolded proteins accumulate in the endoplasmic reticulum. FEBS J 2024; 291:884-896. [PMID: 37997624 DOI: 10.1111/febs.17011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/06/2023] [Accepted: 11/21/2023] [Indexed: 11/25/2023]
Abstract
It is known that oligosaccharyltransferase (OST) has hydrolytic activity toward dolichol-linked oligosaccharides (DLO), which results in the formation of free N-glycans (FNGs), i.e. unconjugated oligosaccharides with structural features similar to N-glycans. The functional importance of this hydrolytic reaction, however, remains unknown. In this study, the hydrolytic activity of OST was characterized in yeast. It was shown that the hydrolytic activity of OST is enhanced in ubiquitin ligase mutants that are involved in endoplasmic reticulum-associated degradation. Interestingly, this enhanced hydrolysis activity is completely suppressed in asparagine-linked glycosylation (alg) mutants, bearing mutations related to the biosynthesis of DLO, indicating that the effect of ubiquitin ligase on OST-mediated hydrolysis is context-dependent. The enhanced hydrolysis activity in ubiquitin ligase mutants was also found to be canceled upon treatment of the cells with dithiothreitol, a reagent that potently induces protein unfolding in the endoplasmic reticulum (ER). Our results clearly suggest that the hydrolytic activity of OST is enhanced under conditions in which the formation of unfolded proteins is promoted in the ER in yeast. The possible role of FNGs on protein folding is discussed.
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Affiliation(s)
- Sheng-Tao Li
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan
| | - Hiroto Hirayama
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan
| | - Chengcheng Huang
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan
| | - Tsugiyo Matsuda
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan
| | - Ritsuko Oka
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan
| | - Takahiro Yamasaki
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan
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