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Chauhan C, Singh P, Muthu SA, Parvez S, Selvapandiyan A, Ahmad B. Plumbagin accelerates serum albumin's amyloid aggregation kinetics and generates fibril polymorphism by inducing non-native β-sheet structures. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141028. [PMID: 38849109 DOI: 10.1016/j.bbapap.2024.141028] [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: 03/08/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
The ligand-induced conformational switch of proteins has great significance in understanding the biophysics and biochemistry of their self-assembly. In this work, we have investigated the ability of plumbagin (PL), a hydroxynaphthoquinone compound found in the root of the medicinal plant Plumbago zeylanica, to modulate aggregation precursor state, aggregation kinetics and generate distinct fibril of human serum albumin (HSA). PL was found to moderately bind (binding constant Ka ∼ 10-4 M-1)) to domain-II of HSA in the stoichiometric ratio of 1:1. We found that PL-HSA complex aggregation was accelerated as compared to that of HSA aggregation and it may be through an independent pathway. We also detected that fibril produced in the presence of PL is wider in diameter, contains a higher amount of β-sheet (∼18%) and disordered (∼46%) structures, and is less stable. We concluded that the acceleration of aggregation reaction and generation of fibril polymorphism was mainly because of the higher extent of unfolding and high content of non-native β-sheet structure in the aggregation precursor state of PL-HSA complex. This study offers opportunities to explore the ability of ligand binding to modulate aggregation reactions and generate polymorphic protein fibrils.
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Affiliation(s)
- Chanchal Chauhan
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India; Department of Molecular Medicine, Jamia Hamdard, New Delhi 10062, India
| | - Poonam Singh
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai 400098, India
| | - Shivani A Muthu
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India; Department of Molecular Medicine, Jamia Hamdard, New Delhi 10062, India
| | - Suhel Parvez
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India
| | | | - Basir Ahmad
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India.
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2
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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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3
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De Luca G, Sancataldo G, Militello B, Vetri V. Surface-catalyzed liquid-liquid phase separation and amyloid-like assembly in microscale compartments. J Colloid Interface Sci 2024; 676:569-581. [PMID: 39053405 DOI: 10.1016/j.jcis.2024.07.135] [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: 04/19/2024] [Revised: 06/24/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Liquid-liquid phase separation is a key phenomenon in the formation of membrane-less structures within the cell, appearing as liquid biomolecular condensates. Protein condensates are the most studied for their biological relevance, and their tendency to evolve, resulting in the formation of aggregates with a high level of order called amyloid. In this study, it is demonstrated that Human Insulin forms micrometric, round amyloid-like structures at room temperature within sub-microliter scale aqueous compartments. These distinctive particles feature a solid core enveloped by a fluid-like corona and form at the interface between the aqueous compartment and the glass coverslip upon which they are cast. Quantitative fluorescence microscopy is used to study in real-time the formation of amyloid-like superstructures. Their formation results driven by liquid-liquid phase separation process that arises from spatially heterogeneous distribution of nuclei at the glass-water interface. The proposed experimental setup allows modifying the surface-to-volume ratio of the aqueous compartments, which affects the aggregation rate and particle size, while also inducing fine alterations in the molecular structures of the final assemblies. These findings enhance the understanding of the factors governing amyloid structure formation, shedding light on the catalytic role of surfaces in this process.
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Affiliation(s)
- Giuseppe De Luca
- Department Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, 16, 90128, Palermo, Italy; Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy.
| | - Giuseppe Sancataldo
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy.
| | - Benedetto Militello
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy; INFN Sezione di Catania, Via Santa Sofia 64, 95123 Catania, Italy.
| | - Valeria Vetri
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy.
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4
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Neupane K, Narayan A, Sen Mojumdar S, Adhikari G, Garen CR, Woodside MT. Direct observation of prion-like propagation of protein misfolding templated by pathogenic mutants. Nat Chem Biol 2024:10.1038/s41589-024-01672-8. [PMID: 39009686 DOI: 10.1038/s41589-024-01672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/06/2024] [Indexed: 07/17/2024]
Abstract
Many neurodegenerative diseases feature misfolded proteins that propagate via templated conversion of natively folded molecules. However, crucial questions about how such prion-like conversion occurs and what drives it remain unsolved, partly because technical challenges have prevented direct observation of conversion for any protein. We observed prion-like conversion in single molecules of superoxide dismutase-1 (SOD1), whose misfolding is linked to amyotrophic lateral sclerosis. Tethering pathogenic misfolded SOD1 mutants to wild-type molecules held in optical tweezers, we found that the mutants vastly increased misfolding of the wild-type molecule, inducing multiple misfolded isoforms. Crucially, the pattern of misfolding was the same in the mutant and converted wild-type domains and varied when the misfolded mutant was changed, reflecting the templating effect expected for prion-like conversion. Ensemble measurements showed decreased enzymatic activity in tethered heterodimers as conversion progressed, mirroring the single-molecule results. Antibodies sensitive to disease-specific epitopes bound to the converted protein, implying that conversion produced disease-relevant misfolded conformers.
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Affiliation(s)
- Krishna Neupane
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Abhishek Narayan
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Supratik Sen Mojumdar
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- Department of Chemistry, Indian Institute of Technology Palakkad, Palakkad, India
| | - Gaurav Adhikari
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Craig R Garen
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada.
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada.
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada.
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5
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Hemagirri M, Chen Y, Gopinath SCB, Sahreen S, Adnan M, Sasidharan S. Crosstalk between protein misfolding and endoplasmic reticulum stress during ageing and their role in age-related disorders. Biochimie 2024; 221:159-181. [PMID: 37918463 DOI: 10.1016/j.biochi.2023.10.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Maintaining the proteome is crucial to retaining cell functionality and response to multiple intrinsic and extrinsic stressors. Protein misfolding increased the endoplasmic reticulum (ER) stress and activated the adaptive unfolded protein response (UPR) to restore cell homeostasis. Apoptosis occurs when ER stress is prolonged or the adaptive response fails. In healthy young cells, the ratio of protein folding machinery to quantities of misfolded proteins is balanced under normal circumstances. However, the age-related deterioration of the complex systems for handling protein misfolding is accompanied by ageing-related disruption of protein homeostasis, which results in the build-up of misfolded and aggregated proteins. This ultimately results in decreased cell viability and forms the basis of common age-related diseases called protein misfolding diseases. Proteins or protein fragments convert from their ordinarily soluble forms to insoluble fibrils or plaques in many of these disorders, which build up in various organs such as the liver, brain, or spleen. Alzheimer's, Parkinson's, type II diabetes, and cancer are diseases in this group commonly manifest in later life. Thus, protein misfolding and its prevention by chaperones and different degradation paths are becoming understood from molecular perspectives. Proteodynamics information will likely affect future interventional techniques to combat cellular stress and support healthy ageing by avoiding and treating protein conformational disorders. This review provides an overview of the diverse proteostasis machinery, protein misfolding, and ER stress involvement, which activates the UPR sensors. Here, we will discuss the crosstalk between protein misfolding and ER stress and their role in developing age-related diseases.
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Affiliation(s)
- Manisekaran Hemagirri
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | - Yeng Chen
- Department of Oral & Craniofacial Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Subash C B Gopinath
- Faculty of Chemical Engineering and Technology, Universiti Malaysia Perlis, Arau, 02600, Malaysia
| | - Sumaira Sahreen
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, P. O. Box 2440, Saudi Arabia.
| | - Sreenivasan Sasidharan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia.
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6
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Nguyen T, Narayanareddy BRJ, Gross SP, Miles CE. Competition between physical search and a weak-to-strong transition rate-limits kinesin binding times. PLoS Comput Biol 2024; 20:e1012158. [PMID: 38768214 PMCID: PMC11142708 DOI: 10.1371/journal.pcbi.1012158] [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: 03/15/2024] [Revised: 05/31/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024] Open
Abstract
The self-organization of cells relies on the profound complexity of protein-protein interactions. Challenges in directly observing these events have hindered progress toward understanding their diverse behaviors. One notable example is the interaction between molecular motors and cytoskeletal systems that combine to perform a variety of cellular functions. In this work, we leverage theory and experiments to identify and quantify the rate-limiting mechanism of the initial association between a cargo-bound kinesin motor and a microtubule track. Recent advances in optical tweezers provide binding times for several lengths of kinesin motors trapped at varying distances from a microtubule, empowering the investigation of competing models. We first explore a diffusion-limited model of binding. Through Brownian dynamics simulations and simulation-based inference, we find this simple diffusion model fails to explain the experimental binding times, but an extended model that accounts for the ADP state of the molecular motor agrees closely with the data, even under the scrutiny of penalizing for additional model complexity. We provide quantification of both kinetic rates and biophysical parameters underlying the proposed binding process. Our model suggests that a typical binding event is limited by ADP state rather than physical search. Lastly, we predict how these association rates can be modulated in distinct ways through variation of environmental concentrations and physical properties.
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Affiliation(s)
- Trini Nguyen
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
| | | | - Steven P. Gross
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, United States of America
- Department of Physics, University of California, Irvine, Irvine, California, United States of America
| | - Christopher E. Miles
- Department of Mathematics, University of California, Irvine, Irvine, California, United States of America
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7
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Juković M, Ratkaj I, Kalafatovic D, Bradshaw NJ. Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation. Biophys Chem 2024; 308:107202. [PMID: 38382283 DOI: 10.1016/j.bpc.2024.107202] [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: 11/29/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.
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Affiliation(s)
- Maja Juković
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Ratkaj
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Daniela Kalafatovic
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
| | - Nicholas J Bradshaw
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
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8
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Solomonov A, Kozell A, Shimanovich U. Designing Multifunctional Biomaterials via Protein Self-Assembly. Angew Chem Int Ed Engl 2024; 63:e202318365. [PMID: 38206201 DOI: 10.1002/anie.202318365] [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: 11/30/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Protein self-assembly is a fundamental biological process where proteins spontaneously organize into complex and functional structures without external direction. This process is crucial for the formation of various biological functionalities. However, when protein self-assembly fails, it can trigger the development of multiple disorders, thus making understanding this phenomenon extremely important. Up until recently, protein self-assembly has been solely linked either to biological function or malfunction; however, in the past decade or two it has also been found to hold promising potential as an alternative route for fabricating materials for biomedical applications. It is therefore necessary and timely to summarize the key aspects of protein self-assembly: how the protein structure and self-assembly conditions (chemical environments, kinetics, and the physicochemical characteristics of protein complexes) can be utilized to design biomaterials. This minireview focuses on the basic concepts of forming supramolecular structures, and the existing routes for modifications. We then compare the applicability of different approaches, including compartmentalization and self-assembly monitoring. Finally, based on the cutting-edge progress made during the last years, we summarize the current knowledge about tailoring a final function by introducing changes in self-assembly and link it to biomaterials' performance.
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Affiliation(s)
- Aleksei Solomonov
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 234 Herzl st., Rehovot, 76100, Israel
| | - Anna Kozell
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 234 Herzl st., Rehovot, 76100, Israel
| | - Ulyana Shimanovich
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 234 Herzl st., Rehovot, 76100, Israel
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9
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Kam A, Loo S, Qiu Y, Liu CF, Tam JP. Ultrafast Biomimetic Oxidative Folding of Cysteine-rich Peptides and Microproteins in Organic Solvents. Angew Chem Int Ed Engl 2024; 63:e202317789. [PMID: 38342764 DOI: 10.1002/anie.202317789] [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: 11/21/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/13/2024]
Abstract
Disulfides in peptides and proteins are essential for maintaining a properly folded structure. Their oxidative folding is invariably performed in an aqueous-buffered solution. However, this process is often slow and can lead to misfolded products. Here, we report a novel concept and strategy that is bio-inspired to mimic protein disulfide isomerase (PDI) by accelerating disulfide exchange rates many thousand-fold. The proposed strategy termed organic oxidative folding is performed under organic solvents to yield correctly folded cysteine-rich microproteins instantaneously without observable misfolded or dead-end products. Compared to conventional aqueous oxidative folding strategies, enormously large rate accelerations up to 113,200-fold were observed. The feasibility and generality of the organic oxidative folding strategy was successfully demonstrated on 15 cysteine-rich microproteins of different hydrophobicity, lengths (14 to 58 residues), and numbers of disulfides (2 to 5 disulfides), producing the native products in a second and in high yield.
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Affiliation(s)
- Antony Kam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Wuzhong No.111, Renai Road, Suzhou, Jiangsu, 215123, People's Republic of China
| | - Shining Loo
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Wisedom Lake Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Wuzhong No. 111, Renai Road, Suzhou, Jiangsu, 215123, People's Republic of China
| | - Yibo Qiu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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10
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Gurubaran IS. Mitochondrial damage and clearance in retinal pigment epithelial cells. Acta Ophthalmol 2024; 102 Suppl 282:3-53. [PMID: 38467968 DOI: 10.1111/aos.16661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 03/13/2024]
Abstract
Age-related macular degeneration (AMD) is a devastating eye disease that causes permanent vision loss in the central part of the retina, known as the macula. Patients with such severe visual loss face a reduced quality of life and are at a 1.5 times greater risk of death compared to the general population. Currently, there is no cure for or effective treatment for dry AMD. There are several mechanisms thought to underlie the disease, for example, ageing-associated chronic oxidative stress, mitochondrial damage, harmful protein aggregation and inflammation. As a way of gaining a better understanding of the molecular mechanisms behind AMD and thus developing new therapies, we have created a peroxisome proliferator-activated receptor gamma coactivator 1-alpha and nuclear factor erythroid 2-related factor 2 (PGC1α/NFE2L2) double-knockout (dKO) mouse model that mimics many of the clinical features of dry AMD, including elevated levels of oxidative stress markers, damaged mitochondria, accumulating lysosomal lipofuscin and extracellular drusen-like structures in retinal pigment epithelial cells (RPE). In addition, a human RPE cell-based model was established to examine the impact of non-functional intracellular clearance systems on inflammasome activation. In this study, we found that there was a disturbance in the autolysosomal machinery responsible for clearing mitochondria in the RPE cells of one-year-old PGC1α/NFE2L2-deficient mice. The confocal immunohistochemical analysis revealed an increase in autophagosome marker microtubule-associated proteins 1A/1B light chain 3B (LC3B) as well as multiple mitophagy markers such as PTE-induced putative kinase 1 (PINK1) and E3 ubiquitin ligase (PARKIN), along with signs of damaged mitochondria. However, no increase in autolysosome formation was detected, nor was there a colocalization of the lysosomal marker LAMP2 or the mitochondrial marker, ATP synthase β. There was an upregulation of late autolysosomal fusion Ras-related protein (Rab7) in the perinuclear space of RPE cells, together with autofluorescent aggregates. Additionally, we observed an increase in the numbers of Toll-like receptors 3 and 9, while those of NOD-like receptor 3 were decreased in PGC1α/NFE2L2 dKO retinal specimens compared to wild-type animals. There was a trend towards increased complement component C5a and increased involvement of the serine protease enzyme, thrombin, in enhancing the terminal pathway producing C5a, independent of C3. The levels of primary acute phase C-reactive protein and receptor for advanced glycation end products were also increased in the PGC1α/NFE2L2 dKO retina. Furthermore, selective proteasome inhibition with epoxomicin promoted both nicotinamide adenine dinucleotide phosphate (NADPH) oxidase and mitochondrial-mediated oxidative stress, leading to the release of mitochondrial DNA to the cytosol, resulting in potassium efflux-dependent activation of the absent in melanoma 2 (AIM2) inflammasome and the subsequent secretion of interleukin-1β in ARPE-19 cells. In conclusion, the data suggest that there is at least a relative decrease in mitophagy, increases in the amounts of C5 and thrombin and decreased C3 levels in this dry AMD-like model. Moreover, selective proteasome inhibition evoked mitochondrial damage and AIM2 inflammasome activation in ARPE-19 cells.
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Affiliation(s)
- Iswariyaraja Sridevi Gurubaran
- Department of Medicine, Clinical Medicine Unit, University of Eastern Finland Institute of Clinical Medicine, Kuopio, Northern Savonia, Finland
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11
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Feng L, Wang G, Song Q, Feng X, Su J, Ji G, Li M. Proteomics revealed an association between ribosome-associated proteins and amyloid beta deposition in Alzheimer's disease. Metab Brain Dis 2024; 39:263-282. [PMID: 38019374 DOI: 10.1007/s11011-023-01330-3] [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: 09/11/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
Most scholars believe that amyloid-beta (Aβ) has the potential to induce apoptosis, stimulate an inflammatory cascade, promote oxidative stress and exacerbate the pathological progression of Alzheimer's disease (AD). Therefore, it is crucial to investigate the deposition of Aβ in AD. At approximately 6 months of age, APP/PS1 double transgenic mice gradually exhibit the development of plaques, as well as spatial and learning impairment. Notably, the hippocampus is specifically affected in the course of AD. Herein, 6-month-old APP/PS1 double transgenic mice were utilized, and the differentially expressed (DE) proteins in the hippocampus were identified and analyzed using 4D label-free quantitative proteomics technology and parallel reaction monitoring (PRM). Compared to wild-type mice, 29 proteins were upregulated and 25 proteins were downregulated in the AD group. Gene Ontology (GO) enrichment analysis of biological processes (BP) indicated that the DE proteins were mainly involved in 'ribosomal large subunit biogenesis'. Molecular function (MF) analysis results were primarily associated with '5.8S rRNA binding' and 'structural constituent of ribosome'. In terms of cellular components (CC), the DE proteins were mainly found in 'polysomal ribosome', 'cytosolic large ribosomal subunit', 'cytosolic ribosome', and 'large ribosomal subunit', among others. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that the results were mainly enriched in the 'Ribosome signaling pathway'. The key target proteins identified were ribosomal protein (Rp)l18, Rpl17, Rpl19, Rpl24, Rpl35, and Rpl6. The PRM verification results were consistent with the findings of the 4D label-free quantitative proteomics analysis. Overall, these findings suggest that Rpl18, Rpl17, Rpl19, Rpl24, Rpl35, and Rpl6 may have potential therapeutic value for the treatment of AD by targeting Aβ.
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Affiliation(s)
- Lina Feng
- Department of Neurology, the Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Guojun Wang
- Department of Neurosurgery, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China
| | - Qile Song
- Department of Neurology, the Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Xiaotong Feng
- Department of Neurology, the Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Jing Su
- Department of Geriatric Cardiovascular, The Affiliated Taian City Central Hospital of Qingdao University, Longtan Road, Taian, 271000, Shandong, China.
| | - Guangcheng Ji
- Department of Neurology, the Third Affiliated Clinical Hospital of the Changchun University of Chinese Medicine, Boshuo Road, Changchun, 130117, Jilin, China.
| | - Mingquan Li
- Department of Neurology, the Third Affiliated Clinical Hospital of the Changchun University of Chinese Medicine, Boshuo Road, Changchun, 130117, Jilin, China.
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12
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Katina N, Marchenkov V, Ryabova N, Ilyina N, Marchenko N, Balobanov V, Finkelstein A. Influence of Amino Acid Substitutions in ApoMb on Different Stages of Unfolding of Amyloids. Molecules 2023; 28:7736. [PMID: 38067466 PMCID: PMC10707739 DOI: 10.3390/molecules28237736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
To date, most research on amyloid aggregation has focused on describing the structure of amyloids and the kinetics of their formation, while the conformational stability of fibrils remains insufficiently explored. The aim of this work was to investigate the effect of amino acid substitutions on the stability of apomyoglobin (ApoMb) amyloids. A study of the amyloid unfolding of ApoMb and its six mutant variants by urea has been carried out. Changes in the structural features of aggregates during unfolding were recorded by far-UV CD and native electrophoresis. It was shown that during the initial stage of denaturation, amyloids' secondary structure partially unfolds. Then, the fibrils undergo dissociation and form intermediate aggregates weighing approximately 1 MDa, which at the last stage of unfolding decompose into 18 kDa monomeric unfolded molecules. The results of unfolding transitions suggest that the stability of the studied amyloids relative to the intermediate aggregates and of the latter relative to unfolded monomers is higher for ApoMb variants with substitutions that increase the hydrophobicity of the residues. The results presented provide a new insight into the mechanism of stabilization of protein aggregates and can serve as a base for further investigations of the amyloids' stability.
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Affiliation(s)
- Natalya Katina
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 142290 Pushchino, Russia
| | - Victor Marchenkov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Natalya Ryabova
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Nelly Ilyina
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Natalia Marchenko
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Vitalii Balobanov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
| | - Alexey Finkelstein
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (V.M.); (N.R.); (N.I.); (N.M.)
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13
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Hardebeck S, Schreiber S, Adick A, Langer K, Jose J. A FRET-Based Assay for the Identification of PCNA Inhibitors. Int J Mol Sci 2023; 24:11858. [PMID: 37511614 PMCID: PMC10380293 DOI: 10.3390/ijms241411858] [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: 07/05/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is the key regulator of human DNA metabolism. One important interaction partner is p15, involved in DNA replication and repair. Targeting the PCNA-p15 interaction is a promising therapeutic strategy against cancer. Here, a Förster resonance energy transfer (FRET)-based assay for the analysis of the PCNA-p15 interaction was developed. Next to the application as screening tool for the identification and characterization of PCNA-p15 interaction inhibitors, the assay is also suitable for the investigation of mutation-induced changes in their affinity. This is particularly useful for analyzing disease associated PCNA or p15 variants at the molecular level. Recently, the PCNA variant C148S has been associated with Ataxia-telangiectasia-like disorder type 2 (ATLD2). ATLD2 is a neurodegenerative disease based on defects in DNA repair due to an impaired PCNA. Incubation time dependent FRET measurements indicated no effect on PCNAC148S-p15 affinity, but on PCNA stability. The impaired stability and increased aggregation behavior of PCNAC148S was confirmed by intrinsic tryptophan fluorescence, differential scanning fluorimetry (DSF) and asymmetrical flow field-flow fractionation (AF4) measurements. The analysis of the disease associated PCNA variant demonstrated the versatility of the interaction assay as developed.
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Affiliation(s)
- Sarah Hardebeck
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, Pharmacampus, 48149 Münster, Germany
| | - Sebastian Schreiber
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, Pharmacampus, 48149 Münster, Germany
| | - Annika Adick
- University of Münster, Institute for Pharmaceutical Technology and Biopharmacy, Pharmacampus, 48149 Münster, Germany
| | - Klaus Langer
- University of Münster, Institute for Pharmaceutical Technology and Biopharmacy, Pharmacampus, 48149 Münster, Germany
| | - Joachim Jose
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, Pharmacampus, 48149 Münster, Germany
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14
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Majid N, Khan RH. Protein aggregation: Consequences, mechanism, characterization and inhibitory strategies. Int J Biol Macromol 2023; 242:125123. [PMID: 37270122 DOI: 10.1016/j.ijbiomac.2023.125123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/01/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023]
Abstract
Proteins play a major role in the regulation of various cellular functions including the synthesis of structural components. But proteins are stable under physiological conditions only. A slight variation in environmental conditions can cost them huge in terms of conformational stability ultimately leading to aggregation. Under normal conditions, aggregated proteins are degraded or removed from the cell by a quality control system including ubiquitin-proteasomal machinery and autophagy. But they are burdened under diseased conditions or are impaired by the aggregated proteins leading to the generation of toxicity. The misfolding and aggregation of protein such as amyloid-β, α-synuclein, human lysozyme etc., are responsible for certain diseases including Alzheimer, Parkinson, and non- neuropathic systemic amyloidosis respectively. Extensive research has been done to find the therapeutics for such diseases but till now we have got only symptomatic treatment that will reduce the disease severity but will not target the initial formation of nucleus responsible for disease progression and propagation. Hence there is an urgent need to develop the drugs targeting the cause of the disease. For this, a wide knowledge related to misfolding and aggregation under the same heading is required as described in this review alongwith the strategies hypothesized and implemented till now. This will contribute a lot to the work of researchers in the field of neuroscience.
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Affiliation(s)
- Nabeela Majid
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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15
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Gupta S, Dasmahapatra AK. Enhanced stability of a disaggregated Aβ fibril on removal of ligand inhibits refibrillation: An all atom Molecular Dynamics simulation study. Int J Biol Macromol 2023; 240:124481. [PMID: 37076062 DOI: 10.1016/j.ijbiomac.2023.124481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
The extraneuronally deposited senile plaques, composed of neurotoxic aggregates of Aβ fibril, define Alzheimer's disease (AD). Natural compounds have been tested for their destabilization potential on Aβ fibril, thereby curing AD. However, the resultant destabilized Aβ fibril, needs to be checked for its irreversibility to the native organized state after removal of the ligand. Herein, we assessed the stability of a destabilized fibril after the ligand (ellagic acid represented as REF) is removed from the complex. The study has been conducted via Molecular Dynamics (MD) simulation of 1 μs for both Aβ-Water (control) and Aβ-REF″ (test or REF removed) system. The increased value of RMSD, Rg, SASA, lower β-sheet content and reduced number of H-bonds explains enhanced destabilization observed in Aβ-REF″ system. The increased inter-chain distance demonstrates breaking of the residual contacts, testifying the drift of terminal chains from the pentamer. The increased SASA along with the ∆Gps(polar solvation energy) accounts for the reduced interaction amongst residues, and more with solvent molecules, governing irreversibility to native state. The higher Gibb's free energy of the misaligned structure of Aβ-REF″ ensures irreversibility to the organized structure due to its inability to cross such high energy barrier. The observed stability of the disaggregated structure, despite ligand elimination, establishes the effectiveness of the destabilization technique as a promising therapeutic approach towards treating AD.
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Affiliation(s)
- Shivani Gupta
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ashok Kumar Dasmahapatra
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; Center for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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16
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Ye J, Zheng J, Lu X, Wu F, Liu N, Dong Y, Shi Q, Xu L, Liu D. Single-Molecular Poly(propylene oxide) (PPO) Nucleus-Guided Assembly for Hydrophobicity-Dependent Molecular Transport in the Nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4537-4543. [PMID: 36926892 DOI: 10.1021/acs.langmuir.3c00447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
By combining DNA nanotechnology and solid-phase nanopore technology, the aggregation behavior of polymer guided by a single-molecular poly(propylene) (PPO) nucleus in a 3D DNA network has been studied. At low temperature, the PPO chain is evenly dispersed in the rigid 3D DNA network; at higher temperature, the PPO chain self-collapses to a single-molecular nucleus; and upon addition of amphiphilic block copolymers below the critical micelle concentration (CMC), the chains tend to aggregate on the isolated hydrophobic nucleus through intermolecular hydrophobic interactions. The process has been characterized by a rheological test and an electrochemical test. This study not only provides a preliminary understanding of the nucleation and growth process of block copolymers but also offers a theoretical basis for the study of protein self-folding and aggregation in the future. On this basis, utilizing this nucleation and growth event, a novel smart nanopore has been developed for hydrophobicity-dependent molecular transport.
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Affiliation(s)
- Jianhan Ye
- Department of Chemistry, Renmin University of China, Beijing 100872, China
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Juanjuan Zheng
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Xin Lu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Fen Wu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Nannan Liu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Yuanchen Dong
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Qian Shi
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Lijin Xu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
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17
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Mehlhoff JD, Ostermeier M. Genes Vary Greatly in Their Propensity for Collateral Fitness Effects of Mutations. Mol Biol Evol 2023; 40:7043719. [PMID: 36798991 PMCID: PMC9999109 DOI: 10.1093/molbev/msad038] [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: 10/24/2022] [Revised: 01/18/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Mutations can have deleterious fitness effects when they decrease protein specific activity or decrease active protein abundance. Mutations will also be deleterious when they cause misfolding or misinteractions that are toxic to the cell (i.e., independent of whether the mutations affect specific activity and abundance). The extent to which protein evolution is shaped by these and other collateral fitness effects is unclear in part because little is known of their frequency and magnitude. Using deep mutational scanning (DMS), we previously found at least 42% of missense mutations in the TEM-1 β-lactamase antibiotic resistance gene cause deleterious collateral fitness effects. Here, we used DMS to comprehensively determine the collateral fitness effects of missense mutations in three genes encoding the antibiotic resistance proteins New Delhi metallo-β-lactamase (NDM-1), chloramphenicol acetyltransferase I (CAT-I), and 2″-aminoglycoside nucleotidyltransferase (AadB). AadB (20%), CAT-I (0.9%), and NDM-1 (0.2%) were less susceptible to deleterious collateral fitness effects than TEM-1 (42%) indicating that genes have different propensities for these effects. As was observed with TEM-1, all the studied deleterious aadB mutants increased aggregation. However, aggregation did not correlate with collateral fitness effects for many of the deleterious mutants of CAT-I and NDM-1. Select deleterious mutants caused unexpected phenotypes to emerge. The introduction of internal start codons in CAT-1 caused loss of the episome and a mutation in aadB made its cognate antibiotic essential for growth. Our study illustrates how the complexity of the cell provides a rich environment for collateral fitness effects and new phenotypes to emerge.
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Affiliation(s)
- Jacob D Mehlhoff
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
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18
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Ajmal MR. Protein Misfolding and Aggregation in Proteinopathies: Causes, Mechanism and Cellular Response. Diseases 2023; 11:diseases11010030. [PMID: 36810544 PMCID: PMC9944956 DOI: 10.3390/diseases11010030] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/02/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
Proteins are central to life functions. Alterations in the structure of proteins are reflected in their function. Misfolded proteins and their aggregates present a significant risk to the cell. Cells have a diverse but integrated network of protection mechanisms. Streams of misfolded proteins that cells are continuously exposed to must be continually monitored by an elaborated network of molecular chaperones and protein degradation factors to control and contain protein misfolding problems. Aggregation inhibition properties of small molecules such as polyphenols are important as they possess other beneficial properties such as antioxidative, anti-inflammatory, and pro-autophagic properties and help neuroprotection. A candidate with such desired features is important for any possible treatment development for protein aggregation diseases. There is a need to study the protein misfolding phenomenon so that we can treat some of the worst kinds of human ailments related to protein misfolding and aggregation.
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Affiliation(s)
- Mohammad Rehan Ajmal
- Physical Biochemistry Research Laboratory, Biochemistry Department, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
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19
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Muschol M, Hoyer W. Amyloid oligomers as on-pathway precursors or off-pathway competitors of fibrils. Front Mol Biosci 2023; 10:1120416. [PMID: 36845541 PMCID: PMC9947291 DOI: 10.3389/fmolb.2023.1120416] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
Amyloid Diseases involve the growth of disease specific proteins into amyloid fibrils and their deposition in protein plaques. Amyloid fibril formation is typically preceded by oligomeric intermediates. Despite significant efforts, the specific role fibrils or oligomers play in the etiology of any given amyloid disease remains controversial. In neurodegenerative disease, though, amyloid oligomers are widely considered critical contributors to disease symptoms. Aside from oligomers as inevitable on-pathway precursors of fibril formation, there is significant evidence for off-pathway oligomer formation competing with fibril growth. The distinct mechanisms and pathways of oligomer formation directly affect our understanding under which conditions oligomers emerge in vivo, and whether their formation is directly coupled to, or distinct from, amyloid fibril formation. In this review, we will discuss the basic energy landscapes underlying the formation of on-pathway vs. off-pathway oligomers, their relation to the related amyloid aggregation kinetics, and their resulting implications for disease etiology. We will review evidence on how differences in the local environment of amyloid assembly can dramatically shift the relative preponderance of oligomers vs. fibrils. Finally, we will comment on gaps in our knowledge of oligomer assembly, of their structure, and on how to assess their relevance to disease etiology.
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Affiliation(s)
- Martin Muschol
- Department of Physics, University of South Florida, Tampa, FL, United States,*Correspondence: Martin Muschol, ; Wolfgang Hoyer,
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany,Institute of Biological Information Processing (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany,*Correspondence: Martin Muschol, ; Wolfgang Hoyer,
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20
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Zhou X, Sinkjær AW, Zhang M, Pinholt HD, Nielsen HM, Hatzakis NS, van de Weert M, Foderà V. Heterogeneous and Surface-Catalyzed Amyloid Aggregation Monitored by Spatially Resolved Fluorescence and Single Molecule Microscopy. J Phys Chem Lett 2023; 14:912-919. [PMID: 36669144 DOI: 10.1021/acs.jpclett.2c03400] [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: 06/17/2023]
Abstract
Amyloid aggregation is associated with many diseases and may also occur in therapeutic protein formulations. Addition of co-solutes is a key strategy to modulate the stability of proteins in pharmaceutical formulations and select inhibitors for drug design in the context of diseases. However, the heterogeneous nature of this multicomponent system in terms of structures and mechanisms poses a number of challenges for the analysis of the chemical reaction. Using insulin as protein system and polysorbate 80 as co-solute, we combine a spatially resolved fluorescence approach with single molecule microscopy and machine learning methods to kinetically disentangle the different contributions from multiple species within a single aggregation experiment. We link the presence of interfaces to the degree of heterogeneity of the aggregation kinetics and retrieve the rate constants and underlying mechanisms for single aggregation events. Importantly, we report that the mechanism of inhibition of the self-assembly process depends on the details of the growth pathways of otherwise macroscopically identical species. This information can only be accessed by the analysis of single aggregate events, suggesting our method as a general tool for a comprehensive physicochemical characterization of self-assembly reactions.
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Affiliation(s)
- Xin Zhou
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Anders Wilgaard Sinkjær
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Henrik Dahl Pinholt
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hanne Mørck Nielsen
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Marco van de Weert
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Vito Foderà
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
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21
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Dasari AKR, Lim KH. CD and Solid-State NMR Studies of Low-Order Oligomers of Transthyretin. Methods Mol Biol 2023; 2551:311-320. [PMID: 36310212 DOI: 10.1007/978-1-0716-2597-2_21] [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] [Indexed: 06/16/2023]
Abstract
Characterization of oligomeric intermediate states populated at an early stage of misfolding and aggregation is essential to understanding molecular mechanism of pathogenic protein aggregation. Growing evidence also suggests that oligomeric species are more toxic than mature fibrillar counterparts. Here, we describe procedures for isolating oligomeric species of an aggregation-prone protein, transthyretin, associated with protein misfolding disorders, including cardiomyopathy and polyneuropathy. We also describe methods for structural studies of the oligomeric species using circular dichroism and solid-state NMR spectroscopy. These methods can be applied to structural characterization of oligomeric intermediates of other aggregation-prone proteins.
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Affiliation(s)
- Anvesh K R Dasari
- Department of Chemistry, East Carolina University, Greenville, NC, USA
| | - Kwang Hun Lim
- Department of Chemistry, East Carolina University, Greenville, NC, USA.
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22
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Pillai M, Jha SK. Multistep molecular mechanism of amyloid-like aggregation of nucleic acid-binding domain of TDP-43. Proteins 2022; 91:649-664. [PMID: 36530161 DOI: 10.1002/prot.26455] [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: 05/02/2022] [Revised: 11/16/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
TDP-43 protein is associated with many neurodegenerative diseases and has been shown to adopt various oligomeric and fibrillar states. However, a detailed kinetic understanding of the structural transformation of the native form of the protein to the fibrillar state is missing. In this study, we delineate the temporal sequence of structural events during the amyloid-like assembly of the functional nucleic acid-binding domain of TDP-43. We kinetically mapped the aggregation process using multiple probes such as tryptophan and thioflavin T (ThT) fluorescence, circular dichroism (CD), and dynamic light scattering (DLS) targeting different structural events. Our data reveal that aggregation occurs in four distinct steps-very fast, fast, slow, and very slow. The "very fast" change results in partially unfolded forms that undergo conformational conversion, oligomerization and bind to ThT in the "fast step" to form higher order intermediates (HOI). The temporal sequence of the formation of ThT binding sites and conformational conversion depends upon the protein concentration. The HOI further undergoes structural rearrangement to form protofibrils in the "slow" step, which, consequently, assembles in the "very slow" step to form an amyloid-like assembly. The spectroscopic properties of the amyloid-like assembly across the protein concentration remain similar. Additionally, we observe no lag phase across protein concentration for all the probes studied, suggesting that the aggregation process follows a linear polymerization reaction. Overall, our study demonstrates that the amyloid-like assembly forms in multiple steps, which is also supported by the temperature dependence of the kinetics.
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Affiliation(s)
- Meenakshi Pillai
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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23
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Qafary M, Rashno F, Khajeh K, Khaledi M, Moosavi-Movahedi AA. Insulin fibrillation: Strategies for inhibition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 175:49-62. [DOI: 10.1016/j.pbiomolbio.2022.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 08/17/2022] [Accepted: 09/08/2022] [Indexed: 04/07/2023]
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24
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Dasari AKR, Yi S, Coats MF, Wi S, Lim KH. Toxic Misfolded Transthyretin Oligomers with Different Molecular Conformations Formed through Distinct Oligomerization Pathways. Biochemistry 2022; 61:2358-2365. [PMID: 36219173 PMCID: PMC9665167 DOI: 10.1021/acs.biochem.2c00390] [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] [Indexed: 11/28/2022]
Abstract
Protein aggregation is initiated by structural changes from native polypeptides to cytotoxic oligomers, which form cross-β structured amyloid. Identification and characterization of oligomeric intermediates are critically important for understanding not only the molecular mechanism of aggregation but also the cytotoxic nature of amyloid oligomers. Preparation of misfolded oligomers for structural characterization is, however, challenging because of their transient, heterogeneous nature. Here, we report two distinct misfolded transthyretin (TTR) oligomers formed through different oligomerization pathways. A pathogenic TTR variant with a strong aggregation propensity (L55P) was used to prepare misfolded oligomers at physiological pH. Our mechanistic studies showed that the full-length TTR initially forms small oligomers, which self-assemble into short protofibrils at later stages. Enzymatic cleavage of the CD loop was also used to induce the formation of N-terminally truncated oligomers, which was detected in ex vivo cardiac TTR aggregates extracted from the tissues of patients. Structural characterization of the oligomers using solid-state nuclear magnetic resonance and circular dichroism revealed that the two TTR misfolded oligomers have distinct molecular conformations. In addition, the proteolytically cleaved TTR oligomers exhibit a higher surface hydrophobicity, suggesting the presence of distinct oligomerization pathways for TTR oligomer formation. Cytotoxicity assays also revealed that the cytotoxicity of cleaved oligomers is stronger than that of the full-length TTR oligomers, indicating that hydrophobicity might be an important property of toxic oligomers. These comparative biophysical analyses suggest that the toxic cleaved TTR oligomers formed through a different misfoling pathway may adopt distinct structural features that produce higher surface hydrophobicity, leading to the stronger cytotoxic activities.
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Affiliation(s)
- Anvesh K. R. Dasari
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Sujung Yi
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Matthew F. Coats
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Sungsool Wi
- Interdisciplinary Magnetic Resonance (CIMAR), National High Magnetic Field Laboratory (NHMFL), 1800 East, Paul Dirac Dr., Tallahassee, FL 32310, USA
| | - Kwang Hun Lim
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
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25
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Rahmatabadi SS, Mobini K, Askari S, Najafian J, Karami K, Soleymani B, Mostafaie A. In silico characterization of fructosyl peptide oxidase properties from Eupenicillium terrenum. J Mol Recognit 2022; 35:e2980. [PMID: 35657361 DOI: 10.1002/jmr.2980] [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: 04/06/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022]
Abstract
Fructosyl peptide oxidase (FPOX) enzyme from Eupenicillium terrenum has a high potential to be applied as a diagnostic enzyme. The aim of the present study is the characterization of FPOX from E. terrenum using different bioinformatics tools. The computational prediction of the RNA and protein secondary structures of FPOX, solubility profile in Escherichia coli, stability, domains, and functional properties were performed. In the FPOX protein, six motifs were detected. The d-amino acid oxidase motif was found as the most important motif that is a FAD-dependent oxidoreductase. The cysteines including 97, 154, 234, 280, and 360 showed a lower score than -10 that have a low possibility for participitation in the formation of the SS bond. The 56.52% of FPOX amino acids are nonpolar. Random coils are dominant in the FPOX sequence, followed by alpha-helix and extended strand. The fpox gene is capable of generating a stable RNA secondary structure (-423.90 kcal/mol) in E. coli. FPOX has a large number of hydrophobic amino acids. FPOX showed a low solubility in E. coli which has several aggregation-prone sites in its 3-D structure. According to the scores, the best mutation candidate for increasing solubility was the conversion of methionine 302 to arginine. The melting temperature of FPOX based on its amino acid sequence was 55°C to 65°C. The amounts of thermodynamic parameters for the FPOX enzyme were -137.4 kcal/mol, -3.59 kcal/(mol K), and -6.8 kcal/mol for standard folding enthalpy, heat capacity, and folding free energy, respectively. In conclusion, the in silico study of proteins can provide a valuable method for better understanding the protein properties and functions for use in our purposes.
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Affiliation(s)
| | - Keivan Mobini
- Department of Hematology, Faculty of Allied Medical Science, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Soudabeh Askari
- Department Biotechnolgy, Applied Razi Biotechnology, Kermanshah, Iran
| | - Javad Najafian
- Department of Biology, Faculty of Basic Science, University of Mazandaran, Baboulsar, Iran
| | - Keyvan Karami
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Bijan Soleymani
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Mostafaie
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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26
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Teixeira JMC, Liu ZH, Namini A, Li J, Vernon RM, Krzeminski M, Shamandy AA, Zhang O, Haghighatlari M, Yu L, Head-Gordon T, Forman-Kay JD. IDPConformerGenerator: A Flexible Software Suite for Sampling the Conformational Space of Disordered Protein States. J Phys Chem A 2022; 126:5985-6003. [PMID: 36030416 PMCID: PMC9465686 DOI: 10.1021/acs.jpca.2c03726] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The power of structural information for informing biological
mechanisms
is clear for stable folded macromolecules, but similar structure–function
insight is more difficult to obtain for highly dynamic systems such
as intrinsically disordered proteins (IDPs) which must be described
as structural ensembles. Here, we present IDPConformerGenerator, a
flexible, modular open-source software platform for generating large
and diverse ensembles of disordered protein states that builds conformers
that obey geometric, steric, and other physical restraints on the
input sequence. IDPConformerGenerator samples backbone phi (φ),
psi (ψ), and omega (ω) torsion angles of relevant sequence
fragments from loops and secondary structure elements extracted from
folded protein structures in the RCSB Protein Data Bank and builds
side chains from robust Monte Carlo algorithms using expanded rotamer
libraries. IDPConformerGenerator has many user-defined options enabling
variable fractional sampling of secondary structures, supports Bayesian
models for assessing the agreement of IDP ensembles for consistency
with experimental data, and introduces a machine learning approach
to transform between internal and Cartesian coordinates with reduced
error. IDPConformerGenerator will facilitate the characterization
of disordered proteins to ultimately provide structural insights into
these states that have key biological functions.
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Affiliation(s)
- João M. C. Teixeira
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Zi Hao Liu
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Ashley Namini
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | | | - Robert M. Vernon
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Mickaël Krzeminski
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Alaa A. Shamandy
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 2E4, Canada
| | | | | | | | | | - Julie D. Forman-Kay
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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27
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Housmans JAJ, Houben B, Monge-Morera M, Asvestas D, Nguyen HH, Tsaka G, Louros N, Carpentier S, Delcour JA, Rousseau F, Schymkowitz J. Investigating the Sequence Determinants of the Curling of Amyloid Fibrils Using Ovalbumin as a Case Study. Biomacromolecules 2022; 23:3779-3797. [PMID: 36027608 DOI: 10.1021/acs.biomac.2c00660] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Highly ordered, straight amyloid fibrils readily lend themselves to structure determination techniques and have therefore been extensively characterized. However, the less ordered curly fibrils remain relatively understudied, and the structural organization underlying their specific characteristics remains poorly understood. We found that the exemplary curly fibril-forming protein ovalbumin contains multiple aggregation prone regions (APRs) that form straight fibrils when isolated as peptides or when excised from the full-length protein through hydrolysis. In the context of the intact full-length protein, however, the regions separating the APRs facilitate curly fibril formation. In fact, a meta-analysis of previously reported curly fibril-forming proteins shows that their inter-APRs are significantly longer and more hydrophobic when compared to straight fibril-forming proteins, suggesting that they may cause strain in the amyloid state. Hence, inter-APRs driving curly fibril formation may not only apply to our model protein but rather constitute a more general mechanism.
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Affiliation(s)
- Joëlle A J Housmans
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Bert Houben
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Margarita Monge-Morera
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Diego Asvestas
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Hung Huy Nguyen
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Grigoria Tsaka
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Sebastien Carpentier
- Facility for Systems Biology Based Mass Spectrometry, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Jan A Delcour
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
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28
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Jangir N, Bangrawa S, Yadav T, Malik S, Alamri AS, Galanakis CM, Singh M, Yadav JK. Isolation and characterization of amyloid-like protein aggregates from soya beans and the effect of low pH and heat treatment on their stability. J Food Biochem 2022; 46:e14369. [PMID: 35945661 DOI: 10.1111/jfbc.14369] [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: 04/07/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/29/2022]
Abstract
Purified soya bean proteins (glycinin and conglycinin) are known to form amyloid-like aggregates in vitro at a higher temperature. Soya beans (chunks) are textured proteinaceous vegetables made from defatted soya flour by heating it above 100°C and extruding under high pressure. Therefore, it was assumed that subjecting the soya bean proteins to high temperatures raises the possibility of forming amyloids or amyloid-like protein aggregates. Hence, the present study aimed to examine the presence of amyloid-like protein aggregates in soya beans. The isolated protein aggregates from hydrated soya beans displayed typical characteristics of amyloids, such as the red shift in the absorption maximum (λmax ) of Congo red (CR), high Thioflavin T (ThT), and 8-Anilinonapthalene-1-sulfonate (ANS) binding, and fibrilar morphology. Furthermore, these aggregates were found to be stable against proteolytic hydrolysis, confirming the specific property of amyloids. The presence of amyloid-like structures in soya beans raises concerns about their implications for human nutrition and health. PRACTICAL APPLICATIONS: Protein aggregation has usually been considered detrimental. The traditional food-processing conditions, such as thermal processing, are associated with protein denaturation and aggregation. The formation of ordered protein aggregates with extensive β-sheet are progressively evident in various protein-rich foods known as amyloid, which expands food safety concerns. Instead, it is also associated with poor nutritional characteristics. The present study concerns the presence of amyloid-like protein aggregates in widely consumed native soya beans, which are manufactured by extensive heat treatment of defatted soy flour. Although there is no indication of their toxicity, these aggregates are found to be proteolytically resistant. The seminal findings in this manuscript suggest that it is time to adapt innovative food processing and supplementation of bioactive molecules that can prevent the formation of such protein aggregates and help maximize the utilization of protein-based nutritional values.
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Affiliation(s)
- Neelam Jangir
- Department of Biotechnology, Central University of Rajasthan, Ajmer, India
| | - Shreya Bangrawa
- Department of Biotechnology, Central University of Rajasthan, Ajmer, India
| | - Tamanna Yadav
- Department of Biotechnology, Central University of Rajasthan, Ajmer, India
| | - Shweta Malik
- Department of Biotechnology, Central University of Rajasthan, Ajmer, India
| | - Abdulhakeem S Alamri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia.,Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | - Charis M Galanakis
- Department of Research & Innovation, Galanakis Laboratories, Chania, Greece.,Department of Biology, College of Science, Taif University, Taif, Saudi Arabia.,Food Waste Recovery Group, ISEKI Food Association, Vienna, Austria
| | - Manish Singh
- Chemical Biology Unit, Institute of Nano Science and Technology, Mohali, India
| | - Jay Kant Yadav
- Department of Biotechnology, Central University of Rajasthan, Ajmer, India
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29
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Yagi-Utsumi M, Kato K. Conformational Variability of Amyloid-β and the Morphological Diversity of Its Aggregates. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154787. [PMID: 35897966 PMCID: PMC9369837 DOI: 10.3390/molecules27154787] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/03/2022]
Abstract
Protein folding is the most fundamental and universal example of biomolecular self-organization and is characterized as an intramolecular process. In contrast, amyloidogenic proteins can interact with one another, leading to protein aggregation. The energy landscape of amyloid fibril formation is characterized by many minima for different competing low-energy structures and, therefore, is much more enigmatic than that of multiple folding pathways. Thus, to understand the entire energy landscape of protein aggregation, it is important to elucidate the full picture of conformational changes and polymorphisms of amyloidogenic proteins. This review provides an overview of the conformational diversity of amyloid-β (Aβ) characterized from experimental and theoretical approaches. Aβ exhibits a high degree of conformational variability upon transiently interacting with various binding molecules in an unstructured conformation in a solution, forming an α-helical intermediate conformation on the membrane and undergoing a structural transition to the β-conformation of amyloid fibrils. This review also outlines the structural polymorphism of Aβ amyloid fibrils depending on environmental factors. A comprehensive understanding of the energy landscape of amyloid formation considering various environmental factors will promote drug discovery and therapeutic strategies by controlling the fibril formation pathway and targeting the consequent morphology of aggregated structures.
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Affiliation(s)
- Maho Yagi-Utsumi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Correspondence: (M.Y.-U.); (K.K.)
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Correspondence: (M.Y.-U.); (K.K.)
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30
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Deol HK, Broom HR, Sienbeneichler B, Lee B, Leonenko Z, Meiering EM. Immature ALS-associated mutant superoxide dismutases form variable aggregate structures through distinct oligomerization processes. Biophys Chem 2022; 288:106844. [DOI: 10.1016/j.bpc.2022.106844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 11/15/2022]
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31
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Abstract
The folding of proteins into their native structure is crucial for the functioning of all biological processes. Molecular chaperones are guardians of the proteome that assist in protein folding and prevent the accumulation of aberrant protein conformations that can lead to proteotoxicity. ATP-independent chaperones do not require ATP to regulate their functional cycle. Although these chaperones have been traditionally regarded as passive holdases that merely prevent aggregation, recent work has shown that they can directly affect the folding energy landscape by tuning their affinity to various folding states of the client. This review focuses on emerging paradigms in the mechanism of action of ATP-independent chaperones and on the various modes of regulating client binding and release.
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Affiliation(s)
- Rishav Mitra
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kevin Wu
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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32
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Meyer N, Arroyo N, Baldelli M, Coquart N, Janot JM, Perrier V, Chinappi M, Picaud F, Torrent J, Balme S. Conical nanopores highlight the pro-aggregating effects of pyrimethanil fungicide on Aβ(1-42) peptides and dimeric splitting phenomena. CHEMOSPHERE 2022; 291:132733. [PMID: 34742766 DOI: 10.1016/j.chemosphere.2021.132733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
The Aβ(1-42) aggregation is a key event in the physiopathology of Alzheimer's disease (AD). Exogenous factors such as environmental pollutants, and more particularly pesticides, can corrupt Aβ(1-42) assembly and could influence the occurrence and pathophysiology of AD. However, pesticide involvement in the early stages of Aβ(1-42) aggregation is still unknown. Here, we employed conical track-etched nanopore in order to analyse the Aβ(1-42) fibril formation in the presence of pyrimethanil, a widely used fungicide belonging to the anilinopyrimidine class. Our results evidenced a pro-aggregating effect of pyrimethanil on Aβ(1-42). Aβ(1-42) assemblies were successfully detected using conical nanopore coated with PEG. Using an analytical model, the large current blockades observed (>0.7) were assigned to species with size close to the sensing pore. The long dwell times (hundreds ms scale) were interpreted by the possible interactions amyloid/PEG using molecular dynamic simulation. Such interaction could leave until splitting phenomena of the dimer structure. Our work also evidences that the pyrimethanil induce an aggregation of Aβ(1-42) mechanism in two steps including the reorganization prior the elongation phase.
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Affiliation(s)
- Nathan Meyer
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Nicolas Arroyo
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 Route de Gray, 25030, Besançon, France
| | - Matteo Baldelli
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Via Del Politecnico 1, 00133, Roma, Italy
| | - Nicolas Coquart
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Jean Marc Janot
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | | | - Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Via Del Politecnico 1, 00133, Roma, Italy
| | - Fabien Picaud
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 Route de Gray, 25030, Besançon, France
| | - Joan Torrent
- INM, University of Montpellier, INSERM, Montpellier, France
| | - Sebastien Balme
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France.
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33
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Han Q, Brown SJ, Drummond CJ, Greaves TL. Protein aggregation and crystallization with ionic liquids: Insights into the influence of solvent properties. J Colloid Interface Sci 2022; 608:1173-1190. [PMID: 34735853 DOI: 10.1016/j.jcis.2021.10.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
Ionic liquids (ILs) have been used in solvents for proteins in many applications, including biotechnology, pharmaceutics, and medicine due to their tunable physicochemical and biological properties. Protein aggregation is often undesirable, and predominantly occurs during bioprocesses, while the aggregation process can be reversible or irreversible and the aggregates formed can be native/non-native and soluble/insoluble. Recent studies have clearly identified key properties of ILs and IL-water mixtures related to protein performance, suggesting the use of the tailorable properties of ILs to inhibit protein aggregation, to promote protein crystallization, and to control protein aggregation pathways. This review discusses the critical properties of IL and IL-water mixtures and presents the latest understanding of the protein aggregation pathways and the development of IL systems that affect or control the protein aggregation process. Through this feature article, we hope to inspire further advances in understanding and new approaches to controlling protein behavior to optimize bioprocesses.
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Affiliation(s)
- Qi Han
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Stuart J Brown
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia.
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Rahman MU, Song K, Da LT, Chen HF. Early aggregation mechanism of Aβ 16-22 revealed by Markov state models. Int J Biol Macromol 2022; 204:606-616. [PMID: 35134456 DOI: 10.1016/j.ijbiomac.2022.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/24/2022] [Accepted: 02/01/2022] [Indexed: 12/19/2022]
Abstract
Aβ16-22 is believed to have critical role in early aggregation of full length amyloids that are associated with the Alzheimer's disease and can aggregate to form amyloid fibrils. However, the early aggregation mechanism is still unsolved. Here, multiple long-term molecular dynamics simulations combining with Markov state model were used to probe the early oligomerization mechanism of Aβ16-22 peptides. The identified dimeric form adopted either globular random-coil or extended β-strand like conformations. The observed dimers of these variants shared many overall conformational characteristics but differed in several aspects at detailed level. In all cases, the most common type of secondary structure was intermolecular antiparallel β-sheets. The inter-state transitions were very frequent ranges from few to hundred nanoseconds. More strikingly, those states which contain fraction of β secondary structure and significant amount of extended coiled structures, therefore exposed to the solvent, were majorly participated in aggregation. The assembly of low-energy dimers, in which the peptides form antiparallel β sheets, occurred by multiple pathways with the formation of an obligatory intermediates. We proposed that these states might facilitate the Aβ16-22 aggregation through a significant component of the conformational selection mechanism, because they might increase the aggregates population by promoting the inter-chain hydrophobic and the hydrogen bond contacts. The formation of early stage antiparallel β sheet structures is critical for oligomerization, and at the same time provided a flat geometry to seed the ordered β-strand packing of the fibrils. Our findings hint at reorganization of this part of the molecule as a potentially critical step in Aβ aggregation and will insight into early oligomerization for large β amyloids.
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Affiliation(s)
- Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kaiyuan Song
- Key Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin-Tai Da
- Key Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Shanghai Center for Bioinformation Technology, Shanghai, 200235, China.
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35
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Rajendran R, Ragavan RP, Al-Sehemi AG, Uddin MS, Aleya L, Mathew B. Current understandings and perspectives of petroleum hydrocarbons in Alzheimer's disease and Parkinson's disease: a global concern. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:10928-10949. [PMID: 35000177 DOI: 10.1007/s11356-021-17931-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Over the last few decades, the global prevalence of neurodevelopmental and neurodegenerative illnesses has risen rapidly. Although the aetiology remains unclear, evidence is mounting that exposure to persistent hydrocarbon pollutants is a substantial risk factor, predisposing a person to neurological diseases later in life. Epidemiological studies correlate environmental hydrocarbon exposure to brain disorders including neuropathies, cognitive, motor and sensory impairments; neurodevelopmental disorders like autism spectrum disorder (ASD); and neurodegenerative disorders like Alzheimer's disease (AD) and Parkinson's disease (PD). Particulate matter, benzene, toluene, ethylbenzene, xylenes, polycyclic aromatic hydrocarbons and endocrine-disrupting chemicals have all been linked to neurodevelopmental problems in all class of people. There is mounting evidence that supports the prevalence of petroleum hydrocarbon becoming neurotoxic and being involved in the pathogenesis of AD and PD. More study is needed to fully comprehend the scope of these problems in the context of unconventional oil and natural gas. This review summarises in vitro, animal and epidemiological research on the genesis of neurodegenerative disorders, highlighting evidence that supports inexorable role of hazardous hydrocarbon exposure in the pathophysiology of AD and PD. In this review, we offer a summary of the existing evidence gathered through a Medline literature search of systematic reviews and meta-analyses of the most important epidemiological studies published so far.
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Affiliation(s)
- Rajalakshmi Rajendran
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, 682041, Kerala, India
| | - Roshni Pushpa Ragavan
- Research Center for Advanced Materials Science, King Khalid University, Abha, 61413, Saudi Arabia.
| | - Abdullah G Al-Sehemi
- Research Center for Advanced Materials Science, King Khalid University, Abha, 61413, Saudi Arabia
- Department of Chemistry, King Khalid University, Abha, 61413, Saudi Arabia
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh
- Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
| | - Lotfi Aleya
- Laboratoire Chrono-Environment, CNRS6249, Universite de Bourgogne Franche-Comte, Besancon, France
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India.
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Stein KC, Morales-Polanco F, van der Lienden J, Rainbolt TK, Frydman J. Ageing exacerbates ribosome pausing to disrupt cotranslational proteostasis. Nature 2022; 601:637-642. [PMID: 35046576 DOI: 10.1038/s41586-021-04295-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 12/01/2021] [Indexed: 02/04/2023]
Abstract
Ageing is accompanied by a decline in cellular proteostasis, which underlies many age-related protein misfolding diseases1,2. Yet, how ageing impairs proteostasis remains unclear. As nascent polypeptides represent a substantial burden on the proteostasis network3, we hypothesized that altered translational efficiency during ageing could help to drive the collapse of proteostasis. Here we show that ageing alters the kinetics of translation elongation in both Caenorhabditis elegans and Saccharomyces cerevisiae. Ribosome pausing was exacerbated at specific positions in aged yeast and worms, including polybasic stretches, leading to increased ribosome collisions known to trigger ribosome-associated quality control (RQC)4-6. Notably, aged yeast cells exhibited impaired clearance and increased aggregation of RQC substrates, indicating that ageing overwhelms this pathway. Indeed, long-lived yeast mutants reduced age-dependent ribosome pausing, and extended lifespan correlated with greater flux through the RQC pathway. Further linking altered translation to proteostasis collapse, we found that nascent polypeptides exhibiting age-dependent ribosome pausing in C. elegans were strongly enriched among age-dependent protein aggregates. Notably, ageing increased the pausing and aggregation of many components of proteostasis, which could initiate a cycle of proteostasis collapse. We propose that increased ribosome pausing, leading to RQC overload and nascent polypeptide aggregation, critically contributes to proteostasis impairment and systemic decline during ageing.
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Affiliation(s)
- Kevin C Stein
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | | | | | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA. .,Department of Genetics, Stanford University, Stanford, CA, USA.
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Gouveia M, Sorčan T, Zemljič-Jokhadar Š, Travasso RDM, Liović M. A mathematical model for the dependence of keratin aggregate formation on the quantity of mutant keratin expressed in EGFP-K14 R125P keratinocytes. PLoS One 2021; 16:e0261227. [PMID: 34962936 PMCID: PMC8714116 DOI: 10.1371/journal.pone.0261227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/24/2021] [Indexed: 11/18/2022] Open
Abstract
We examined keratin aggregate formation and the possible mechanisms involved. With this aim, we observed the effect that different ratios between mutant and wild-type keratins expressed in cultured keratinocytes may have on aggregate formation in vitro, as well as how keratin aggregate formation affects the mechanical properties of cells at the cell cortex. To this end we prepared clones with expression rates as close as possible to 25%, 50% and 100% of the EGFP-K14 proteins (either WT or R125P and V270M mutants). Our results showed that only in the case of the 25% EGFP-K14 R125P mutant significant differences could be seen. Namely, we observed in this case the largest accumulation of keratin aggregates and a significant reduction in cell stiffness. To gain insight into the possible mechanisms behind this observation, we extended our previous mathematical model of keratin dynamics by implementing a more complex reaction network that considers the coexistence of wild-type and mutant keratins in the cell. The new model, consisting of a set of coupled, non-linear, ordinary differential equations, allowed us to draw conclusions regarding the relative amounts of intermediate filaments and aggregates in cells, and suggested that aggregate formation by asymmetric binding between wild-type and mutant keratins could explain the data obtained on cells grown in culture.
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Affiliation(s)
- Marcos Gouveia
- Department of Physics, CFisUC, Center of Physics of the University of Coimbra, University of Coimbra, Coimbra, Portugal
- * E-mail: (MG); (RDMT); (ML)
| | | | - Špela Zemljič-Jokhadar
- Faculty of Medicine, Institute for Biophysics, University of Ljubljana, Ljubljana, Slovenia
| | - Rui D. M. Travasso
- Department of Physics, CFisUC, Center of Physics of the University of Coimbra, University of Coimbra, Coimbra, Portugal
- * E-mail: (MG); (RDMT); (ML)
| | - Mirjana Liović
- Faculty of Medicine, Medical Center for Molecular Biology, Institute for Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
- * E-mail: (MG); (RDMT); (ML)
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Turkez H, Arslan ME, Barboza JN, Kahraman CY, de Sousa DP, Mardinoğlu A. Therapeutic Potential of Ferulic Acid in Alzheimer's Disease. Curr Drug Deliv 2021; 19:860-873. [PMID: 34963433 DOI: 10.2174/1567201819666211228153801] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/16/2021] [Accepted: 10/27/2021] [Indexed: 11/22/2022]
Abstract
Alzheimer's Disease (AD) is one of the most important neurodegenerative diseases and it covers 60% of whole dementia cases. AD is a constantly progressing neurodegenerative disease as a result of the production of β-amyloid (Aβ) protein and the accumulation of hyper-phosphorylated Tau protein; it causes breakages in the synaptic bonds and neuronal deaths to a large extent. Millions of people worldwide suffer from AD because there is no definitive drug for disease prevention, treatment or slowdown. Over the last decade, multiple target applications have been developed for AD treatments. These targets include Aβ accumulations, hyper-phosphorylated Tau proteins, mitochondrial dysfunction, and oxidative stress resulting in toxicity. Various natural or semisynthetic antioxidant formulations have been shown to protect brain cells from Aβ induced toxicity and provide promising potentials for AD treatment. Ferulic acid (FA), a high-capacity antioxidant molecule, is naturally synthesized from certain plants. FA has been shown to have different substantial biological properties, such as anticancer, antidiabetic, antimicrobial, anti-inflammatory, hepatoprotective, and cardioprotective actions, etc. Furthermore, FA exerted neuroprotection via preventing Aβ-fibril formation, acting as an anti-inflammatory agent, and inhibiting free radical generation and acetylcholinesterase (AChE) enzyme activity. In this review, we present key biological roles of FA and several FA derivatives in Aβ-induced neurotoxicity, protection against free radical attacks, and enzyme inhibitions and describe them as possible therapeutic agents for the treatment of AD.
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Affiliation(s)
- Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, 25240, Erzurum, Turkey
- Department of Pharmacy, University G. d'Annunzio Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Mehmet Enes Arslan
- Department of Molecular Biology and Genetics, Erzurum Technical University, 25200, Erzurum, Turkey
| | - Joice Nascimento Barboza
- Department of Pharmaceutical Sciences, Federal University of Paraíba, 58051-970, João Pessoa, PB, Brazil
| | - Cigdem Yuce Kahraman
- Department of Medical Genetics, Faculty of Medicine, Atatürk University, 25240, Erzurum, Turkey
| | - Damiao Pergentino de Sousa
- Department of Pharmaceutical Sciences, Federal University of Paraíba, 58051-970, João Pessoa, PB, Brazil
| | - Adil Mardinoğlu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, SE-17121, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, United Kingdom
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Lendel C, Solin N. Protein nanofibrils and their use as building blocks of sustainable materials. RSC Adv 2021; 11:39188-39215. [PMID: 35492452 PMCID: PMC9044473 DOI: 10.1039/d1ra06878d] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/25/2021] [Indexed: 12/21/2022] Open
Abstract
The development towards a sustainable society requires a radical change of many of the materials we currently use. Besides the replacement of plastics, derived from petrochemical sources, with renewable alternatives, we will also need functional materials for applications in areas ranging from green energy and environmental remediation to smart foods. Proteins could, with their intriguing ability of self-assembly into various forms, play important roles in all these fields. To achieve that, the code for how to assemble hierarchically ordered structures similar to the protein materials found in nature must be cracked. During the last decade it has been demonstrated that amyloid-like protein nanofibrils (PNFs) could be a steppingstone for this task. PNFs are formed by self-assembly in water from a range of proteins, including plant resources and industrial side streams. The nanofibrils display distinct functional features and can be further assembled into larger structures. PNFs thus provide a framework for creating ordered, functional structures from the atomic level up to the macroscale. This review address how industrial scale protein resources could be transformed into PNFs and further assembled into materials with specific mechanical and functional properties. We describe what is required from a protein to form PNFs and how the structural properties at different length scales determine the material properties. We also discuss potential chemical routes to modify the properties of the fibrils and to assemble them into macroscopic structures.
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Affiliation(s)
- Christofer Lendel
- Department of Chemistry, KTH Royal Institute of Technology Teknikringen 30 SE-100 44 Stockholm Sweden
| | - Niclas Solin
- Department of Physics, Chemistry, and Biology, Electronic and Photonic Materials, Biomolecular and Organic Electronics, Linköping University Linköping 581 83 Sweden
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Samanta N, Ribeiro SS, Becker M, Laborie E, Pollak R, Timr S, Sterpone F, Ebbinghaus S. Sequestration of Proteins in Stress Granules Relies on the In-Cell but Not the In Vitro Folding Stability. J Am Chem Soc 2021; 143:19909-19918. [PMID: 34788540 DOI: 10.1021/jacs.1c09589] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Stress granules (SGs) are among the most studied membraneless organelles that form upon heat stress (HS) to sequester unfolded, misfolded, or aggregated protein, supporting protein quality control (PQC) clearance. The folding states that are primarily associated with SGs, as well as the function of the phase separated environment in adjusting the energy landscapes, remain unknown. Here, we investigate the association of superoxide dismutase 1 (SOD1) proteins with different folding stabilities and aggregation propensities with condensates in cells, in vitro and by simulation. We find that irrespective of aggregation the folding stability determines the association of SOD1 with SGs in cells. In vitro and in silico experiments however suggest that the increased flexibility of the unfolded state constitutes only a minor driving force to associate with the dynamic biomolecular network of the condensate. Specific protein-protein interactions in the cytoplasm in comparison to SGs determine the partitioning of folding states between the respective phases during HS.
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Affiliation(s)
- Nirnay Samanta
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
| | - Sara S Ribeiro
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
| | - Mailin Becker
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
| | - Emeline Laborie
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, Paris 75005, France
| | - Roland Pollak
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
| | - Stepan Timr
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, Paris 75005, France.,J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejskova 2155/3, Prague 8 182 23, Czech Republic
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, Paris 75005, France
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
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Ribeiro SS, Castro TG, Gomes CM, Marcos JC. Hofmeister effects on protein stability are dependent on the nature of the unfolded state. Phys Chem Chem Phys 2021; 23:25210-25225. [PMID: 34730580 DOI: 10.1039/d1cp02477a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interpretation of a salt's effect on protein stability traditionally discriminates low concentration regimes (<0.3 M), dominated by electrostatic forces, and high concentration regimes, generally described by ion-specific Hofmeister effects. However, increased theoretical and experimental studies have highlighted observations of the Hofmeister phenomena at concentration ranges as low as 0.001 M. Reasonable quantitative predictions of such observations have been successfully achieved throughout the inclusion of ion dispersion forces in classical electrostatic theories. This molecular description is also on the basis of quantitative estimates obtained resorting to surface/bulk solvent partition models developed for ion-specific Hofmeister effects. However, the latter are limited by the availability of reliable structures representative of the unfolded state. Here, we use myoglobin as a model to explore how ion-dependency on the nature of the unfolded state affects protein stability, combining spectroscopic techniques with molecular dynamic simulations. To this end, the thermal and chemical stability of myoglobin was assessed in the presence of three different salts (NaCl, (NH4)2SO4 and Na2SO4), at physiologically relevant concentrations (0-0.3 M). We observed mild destabilization of the native state induced by each ion, attributed to unfavorable neutralization and hydrogen-bonding with the protein side-chains. Both effects, combined with binding of Na+, Cl- and SO42- to the thermally unfolded state, resulted in an overall destabilization of the protein. Contrastingly, ion binding was hindered in the chemically unfolded conformation, due to occupation of the binding sites by urea molecules. Such mechanistic action led to a lower degree of destabilization, promoting surface tension effects that stabilized myoglobin according to the Hofmeister series. Therefore, we demonstrate that Hofmeister effects on protein stability are modulated by the heterogeneous physico-chemical nature of the unfolded state. Altogether, our findings evidence the need to characterize the structure of the unfolded state when attempting to dissect the molecular mechanisms underlying the effects of salts on protein stability.
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Affiliation(s)
- Sara S Ribeiro
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Tarsila G Castro
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências and Departamento de Química e Bioquímica, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - João C Marcos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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de Andrade DX, Alves ED, de Almeida AR, Colherinhas G. Laminar peptide structure: Energetic and structural evaluation using molecular dynamics. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Marchenkov V, Ryabova N, Balobanov V, Glukhov A, Ilyina N, Katina N. Under Conditions of Amyloid Formation Bovine Carbonic Anhydrase B Undergoes Fragmentation by Acid Hydrolysis. Biomolecules 2021; 11:1608. [PMID: 34827606 PMCID: PMC8615856 DOI: 10.3390/biom11111608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/23/2021] [Accepted: 10/28/2021] [Indexed: 11/23/2022] Open
Abstract
The development of many severe human diseases is associated with the formation of amyloid fibrils. Most of the available information on the process of amyloid formation has been obtained from studies of small proteins and peptides, wherein the features of complex proteins' aggregation remain insufficiently investigated. Our work aimed to research the amyloid aggregation of a large model protein, bovine carbonic anhydrase B (BCAB). It has previously been demonstrated that, when exposed to an acidic pH and elevated temperature, this protein forms amyloid fibrils. Here, we show that, under these conditions and before amyloid formation, BCAB undergoes fragmentation by acid hydrolysis to give free individual peptides and associated peptides. Fragments in associates contain a pronounced secondary structure and act as the main precursor of amyloid fibrils, wherein free peptides adopt mostly unstructured conformation and form predominantly irregular globular aggregates. Reduced acidity decreases the extent of acid hydrolysis, causing BCAB to form amorphous aggregates lacking the thioflavin T binding β-structure. The presented results provide new information on BCAB amyloid formation and show the importance of protein integrity control when working even in mildly acidic conditions.
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Affiliation(s)
| | | | | | | | - Nelly Ilyina
- Institute of Protein Research RAS, 142290 Pushchino, Russia
| | - Natalya Katina
- Institute of Protein Research RAS, 142290 Pushchino, Russia
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44
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Sulatskaya AI, Kosolapova AO, Bobylev AG, Belousov MV, Antonets KS, Sulatsky MI, Kuznetsova IM, Turoverov KK, Stepanenko OV, Nizhnikov AA. β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis. Int J Mol Sci 2021; 22:11316. [PMID: 34768745 PMCID: PMC8582884 DOI: 10.3390/ijms222111316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 01/17/2023] Open
Abstract
Insoluble protein aggregates with fibrillar morphology called amyloids and β-barrel proteins both share a β-sheet-rich structure. Correctly folded β-barrel proteins can not only function in monomeric (dimeric) form, but also tend to interact with one another-followed, in several cases, by formation of higher order oligomers or even aggregates. In recent years, findings proving that β-barrel proteins can adopt cross-β amyloid folds have emerged. Different β-barrel proteins were shown to form amyloid fibrils in vitro. The formation of functional amyloids in vivo by β-barrel proteins for which the amyloid state is native was also discovered. In particular, several prokaryotic and eukaryotic proteins with β-barrel domains were demonstrated to form amyloids in vivo, where they participate in interspecies interactions and nutrient storage, respectively. According to recent observations, despite the variety of primary structures of amyloid-forming proteins, most of them can adopt a conformational state with the β-barrel topology. This state can be intermediate on the pathway of fibrillogenesis ("on-pathway state"), or can be formed as a result of an alternative assembly of partially unfolded monomers ("off-pathway state"). The β-barrel oligomers formed by amyloid proteins possess toxicity, and are likely to be involved in the development of amyloidoses, thus representing promising targets for potential therapy of these incurable diseases. Considering rapidly growing discoveries of the amyloid-forming β-barrels, we may suggest that their real number and diversity of functions are significantly higher than identified to date, and represent only "the tip of the iceberg". Here, we summarize the data on the amyloid-forming β-barrel proteins, their physicochemical properties, and their biological functions, and discuss probable means and consequences of the amyloidogenesis of these proteins, along with structural relationships between these two widespread types of β-folds.
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Affiliation(s)
- Anna I. Sulatskaya
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anastasiia O. Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia;
| | - Mikhail V. Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Maksim I. Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia;
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Olesya V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
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45
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Foley AR, Raskatov JA. Understanding and controlling amyloid aggregation with chirality. Curr Opin Chem Biol 2021; 64:1-9. [PMID: 33610939 PMCID: PMC8368077 DOI: 10.1016/j.cbpa.2021.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 12/22/2022]
Abstract
Amyloid aggregation and human disease are inextricably linked. Examples include Alzheimer disease, Parkinson disease, and type II diabetes. While seminal advances on the mechanistic understanding of these diseases have been made over the last decades, controlling amyloid fibril formation still represents a challenge, and it is a subject of active research. In this regard, chiral modifications have increasingly been proved to offer a particularly well-suited approach toward accessing to previously unknown aggregation pathways and to provide with novel insights on the biological mechanisms of action of amyloidogenic peptides and proteins. Here, we summarize recent advances on how the use of mirror-image peptides/proteins and d-amino acid incorporations have helped modulate amyloid aggregation, offered new mechanistic tools to study cellular interactions, and allowed us to identify key positions within the peptide/protein sequence that influence amyloid fibril growth and toxicity.
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Affiliation(s)
- Alejandro R Foley
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jevgenij A Raskatov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
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Sheikh AM, Wada Y, Tabassum S, Inagaki S, Mitaki S, Yano S, Nagai A. Aggregation of Cystatin C Changes Its Inhibitory Functions on Protease Activities and Amyloid β Fibril Formation. Int J Mol Sci 2021; 22:ijms22189682. [PMID: 34575849 PMCID: PMC8465189 DOI: 10.3390/ijms22189682] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Cystatin C (CST3) is an endogenous cysteine protease inhibitor, which is implicated in cerebral amyloid angiopathy (CAA). In CAA, CST3 is found to be aggregated. The purpose of this study is to investigate whether this aggregation could alter the activity of the protein relevant to the molecular pathology of CAA. A system of CST3 protein aggregation was established, and the aggregated protein was characterized. The results showed that CST3 aggregated both at 80 °C without agitation, and at 37 °C with agitation in a time-dependent manner. However, the levels of aggregation were high and appeared earlier at 80 °C. Dot-blot immunoassay for oligomers revealed that CST3 could make oligomeric aggregates at the 37 °C condition. Electron microscopy showed that CST3 could make short fibrillary aggregates at 37 °C. Cathepsin B activity assay demonstrated that aggregated CST3 inhibited the enzyme activity less efficiently at pH 5.5. At 7.4 pH, it lost the inhibitory properties almost completely. In addition, aggregated CST3 did not inhibit Aβ1-40 fibril formation, rather, it slightly increased it. CST3 immunocytochemistry showed that the protein was positive both in monomeric and aggregated CST3-treated neuronal culture. However, His6 immunocytochemistry revealed that the internalization of exogenous recombinant CST3 by an astrocytoma cell culture was higher when the protein was aggregated compared to its monomeric form. Finally, MTT cell viability assay showed that the aggregated form of CST3 was more toxic than the monomeric form. Thus, our results suggest that aggregation may result in a loss-of-function phenotype of CST3, which is toxic and responsible for cellular degeneration.
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Affiliation(s)
- Abdullah Md. Sheikh
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya Cho, Izumo 693-8501, Japan; (A.M.S.); (S.T.); (S.Y.)
| | - Yasuko Wada
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya Cho, Izumo 693-8501, Japan; (Y.W.); (S.I.); (S.M.)
| | - Shatera Tabassum
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya Cho, Izumo 693-8501, Japan; (A.M.S.); (S.T.); (S.Y.)
| | - Satoshi Inagaki
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya Cho, Izumo 693-8501, Japan; (Y.W.); (S.I.); (S.M.)
| | - Shingo Mitaki
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya Cho, Izumo 693-8501, Japan; (Y.W.); (S.I.); (S.M.)
| | - Shozo Yano
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya Cho, Izumo 693-8501, Japan; (A.M.S.); (S.T.); (S.Y.)
| | - Atsushi Nagai
- Department of Laboratory Medicine, Faculty of Medicine, Shimane University, 89-1 Enya Cho, Izumo 693-8501, Japan; (A.M.S.); (S.T.); (S.Y.)
- Department of Neurology, Faculty of Medicine, Shimane University, 89-1 Enya Cho, Izumo 693-8501, Japan; (Y.W.); (S.I.); (S.M.)
- Correspondence: ; Tel./Fax: +81-0853-20-2198
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Rice LJ, Ecroyd H, van Oijen AM. Illuminating amyloid fibrils: Fluorescence-based single-molecule approaches. Comput Struct Biotechnol J 2021; 19:4711-4724. [PMID: 34504664 PMCID: PMC8405898 DOI: 10.1016/j.csbj.2021.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/15/2022] Open
Abstract
The aggregation of proteins into insoluble filamentous amyloid fibrils is a pathological hallmark of neurodegenerative diseases that include Parkinson's disease and Alzheimer's disease. Since the identification of amyloid fibrils and their association with disease, there has been much work to describe the process by which fibrils form and interact with other proteins. However, due to the dynamic nature of fibril formation and the transient and heterogeneous nature of the intermediates produced, it can be challenging to examine these processes using techniques that rely on traditional ensemble-based measurements. Single-molecule approaches overcome these limitations as rare and short-lived species within a population can be individually studied. Fluorescence-based single-molecule methods have proven to be particularly useful for the study of amyloid fibril formation. In this review, we discuss the use of different experimental single-molecule fluorescence microscopy approaches to study amyloid fibrils and their interaction with other proteins, in particular molecular chaperones. We highlight the mechanistic insights these single-molecule techniques have already provided in our understanding of how fibrils form, and comment on their potential future use in studying amyloid fibrils and their intermediates.
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Affiliation(s)
- Lauren J. Rice
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Antoine M. van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
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48
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Dynamic adsorption and interfacial rheology of whey protein isolate at oil-water interfaces: Effects of protein concentration, pH and heat treatment. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.106640] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Phyo P, Zhao X, Templeton AC, Xu W, Cheung JK, Su Y. Understanding molecular mechanisms of biologics drug delivery and stability from NMR spectroscopy. Adv Drug Deliv Rev 2021; 174:1-29. [PMID: 33609600 DOI: 10.1016/j.addr.2021.02.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/20/2021] [Accepted: 02/07/2021] [Indexed: 02/06/2023]
Abstract
Protein therapeutics carry inherent limitations of membrane impermeability and structural instability, despite their predominant role in the modern pharmaceutical market. Effective formulations are needed to overcome physiological and physicochemical barriers, respectively, for improving bioavailability and stability. Knowledge of membrane affinity, cellular internalization, encapsulation, and release of drug-loaded carrier vehicles uncover the structural basis for designing and optimizing biopharmaceuticals with enhanced delivery efficiency and therapeutic efficacy. Understanding stabilizing and destabilizing interactions between protein drugs and formulation excipients provide fundamental mechanisms for ensuring the stability and quality of biological products. This article reviews the molecular studies of biologics using solution and solid-state NMR spectroscopy on structural attributes pivotal to drug delivery and stability. In-depth investigation of the structure-function relationship of drug delivery systems based on cell-penetrating peptides, lipid nanoparticles and polymeric colloidal, and biophysical and biochemical stability of peptide, protein, monoclonal antibody, and vaccine, as the integrative efforts on drug product design, will be elaborated.
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Affiliation(s)
- Pyae Phyo
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Xi Zhao
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Allen C Templeton
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Wei Xu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Jason K Cheung
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States.
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Perez-Puyana V, Wieringa P, Guerrero A, Romero A, Moroni L. (Macro)Molecular Imprinting of Proteins on PCL Electrospun Scaffolds. ACS APPLIED MATERIALS & INTERFACES 2021; 13:29293-29302. [PMID: 34128651 PMCID: PMC8289240 DOI: 10.1021/acsami.1c04022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/02/2021] [Indexed: 06/12/2023]
Abstract
Biological recognition sites are very useful for biomedical purposes and, more specifically, for polymeric scaffolds. However, synthetic polymers are not capable of providing specific biological recognition sites. To solve this inconvenience, functionalization of biological moieties is typically performed, oftentimes via peptide binding. In this sense, the main task is capturing the biological complexity of a protein. This study proposes a possible alternative solution to this challenge. Our approach is based on the combination of molecular imprinting (MI) and electrospinning processes. We propose here an alternative MI approach with polymeric structures, instead of using cross-linkers and monomers as conventionally performed. Different PCL-protein scaffolds were produced via electrospinning before performing MI. Gelatin, collagen, and elastin were used as proteins. Results evidenced that the MI process conducted with PCL electrospun membranes was carried out with ionic interactions between the desired molecules and the recognition sites formed. In addition, it has been proved that MI was more efficient when using gelatin as a template. This approach opens a new stage in the development of recognition sites in scaffolds obtained with synthetic polymers and their application for biomedical purposes.
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Affiliation(s)
- Victor Perez-Puyana
- Departamento
de Ingeniería Química, Universidad
de Sevilla, Facultad de Química, Escuela Politécnica
Superior, 41012 Sevilla, Spain
- Department
of Complex Tissue Regeneration, MERLN Institute
for Technology-Inspired Regenerative Medicine, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Paul Wieringa
- Department
of Complex Tissue Regeneration, MERLN Institute
for Technology-Inspired Regenerative Medicine, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Antonio Guerrero
- Departamento
de Ingeniería Química, Universidad
de Sevilla, Facultad de Química, Escuela Politécnica
Superior, 41012 Sevilla, Spain
| | - Alberto Romero
- Departamento
de Ingeniería Química, Universidad
de Sevilla, Facultad de Química, Escuela Politécnica
Superior, 41012 Sevilla, Spain
| | - Lorenzo Moroni
- Department
of Complex Tissue Regeneration, MERLN Institute
for Technology-Inspired Regenerative Medicine, Maastricht University, 6200 MD Maastricht, The Netherlands
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