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Sun Y, Shi Y, Li C, Shi H. Histidine Protonation Behaviors on Structural Properties and Aggregation Properties of Aβ(1-42) Mature Fibril: Approaching by Edge Effects. J Phys Chem B 2024; 128:7341-7349. [PMID: 39018428 DOI: 10.1021/acs.jpcb.4c02343] [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: 07/19/2024]
Abstract
The histidine behavior plays a crucial role in the structural and aggregation properties of protein folding and misfolding. Understanding the histidine behavior at the edge of the protein structure is critical for finding ways to disrupt fibril elongation and growth, but this impact remains poorly understood. In the current study, we used molecular dynamics simulations to investigate the edge substitution effect of histidine protonation on the structural and aggregation properties. Our data showed that ΔG1 contributed the most to binding affinity compared to ΔG2 and ΔG3. The different protonation states at the edge chain significantly impacted the secondary structure properties of the edge chain. Specifically, we found that such protonation behavior significantly affected specific regions, particularly the N-terminus (G9-Q15) and C-terminus (K28-A30). Further analysis confirmed that H6, H13, and H14 were directly involved in H-bonding networks with the C1_H14//C2_H13 interchain interactions critical for maintaining the interchain stability. Furthermore, we confirmed that H6, H13, and H14 were directly involved in the loss of the carbon skeleton contact in the N-terminus. Our findings indicate that the edge condition is more susceptible to changes in structural properties than the middle condition. The current study is helpful for understanding the histidine behavior hypothesis in related misfolding diseases.
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Affiliation(s)
- Yue Sun
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Yaru Shi
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Changgui Li
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Hu Shi
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
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Chauhan R, Navale GR, Saini S, Panwar A, Kukreti P, Saini R, Roy P, Ghosh K. Modulating the aggregation of human prion protein PrP 106-126 by an indole-based cyclometallated palladium complex. Dalton Trans 2024; 53:11995-12006. [PMID: 38963284 DOI: 10.1039/d4dt00704b] [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: 07/05/2024]
Abstract
The spontaneous aggregation of infectious or misfolded forms of prion protein is known to be responsible for neurotoxicity in brain cells, which ultimately leads to the progression of prion disorders. Bovine spongiform encephalopathy (BSE) in animals and Creutzfeldt-Jakob disease (CJD) in humans are glaring examples in this regard. Square-planar complexes with labile ligands and indole-based compounds are found to be efficiently inhibitory against protein aggregation. Herein, we report the synthesis of an indole-based cyclometallated palladium complex. The ligand and complex were characterized by various spectroscopic techniques such as UV-visible, NMR, IR, and HRMS. The molecular structure of the complex was confirmed by single-crystal X-ray crystallography. The interaction of the complex with PrP106-126 was studied using UV-visible spectroscopy, CD spectroscopy, MALDI-TOF MS, and molecular docking. The inhibition effects of the complex on the PrP106-126 aggregation, fibrillization and amyloid formation phenomena were analysed through the ThT assay, CD, TEM and AFM. The effect of the complex on the aggregation process of PrP106-126 was determined kinetically through the ThT assay. The complex presented high binding affinity with the peptide and influenced the peptide's conformation and aggregation in different modes of binding. Furthermore, the MTT assay on neuronal HT-22 cells showed considerable protective properties of the complex against PrP106-126-mediated cytotoxicity. These findings suggest that the compound influences peptide aggregation in different ways, and the anti-aggregation action is primarily associated with the metal's physicochemical properties and the reactivity rather than the ligand. As a result, we propose that this compound be investigated as a potential therapeutic molecule in metallopharmaceutical research to treat prion disease (PD).
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Affiliation(s)
- Rahul Chauhan
- Department of Chemistry, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India.
| | - Govinda R Navale
- Department of Chemistry, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India.
| | - Saakshi Saini
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India
| | - Abhishek Panwar
- Department of Chemistry, National Institute of Technology Manipur, Langol 795004, India
| | - Prashant Kukreti
- Department of Chemistry, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India.
| | - Rajat Saini
- Department of Chemistry, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India.
| | - Partha Roy
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India
| | - Kaushik Ghosh
- Department of Chemistry, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India.
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India
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Kell DB, Lip GYH, Pretorius E. Fibrinaloid Microclots and Atrial Fibrillation. Biomedicines 2024; 12:891. [PMID: 38672245 PMCID: PMC11048249 DOI: 10.3390/biomedicines12040891] [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: 03/08/2024] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Atrial fibrillation (AF) is a comorbidity of a variety of other chronic, inflammatory diseases for which fibrinaloid microclots are a known accompaniment (and in some cases, a cause, with a mechanistic basis). Clots are, of course, a well-known consequence of atrial fibrillation. We here ask the question whether the fibrinaloid microclots seen in plasma or serum may in fact also be a cause of (or contributor to) the development of AF. We consider known 'risk factors' for AF, and in particular, exogenous stimuli such as infection and air pollution by particulates, both of which are known to cause AF. The external accompaniments of both bacterial (lipopolysaccharide and lipoteichoic acids) and viral (SARS-CoV-2 spike protein) infections are known to stimulate fibrinaloid microclots when added in vitro, and fibrinaloid microclots, as with other amyloid proteins, can be cytotoxic, both by inducing hypoxia/reperfusion and by other means. Strokes and thromboembolisms are also common consequences of AF. Consequently, taking a systems approach, we review the considerable evidence in detail, which leads us to suggest that it is likely that microclots may well have an aetiological role in the development of AF. This has significant mechanistic and therapeutic implications.
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kongens Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa
| | - Gregory Y. H. Lip
- Liverpool Centre for Cardiovascular Science at University of Liverpool, Liverpool John Moores University and Liverpool Heart and Chest Hospital, Liverpool L7 8TX, UK;
- Danish Center for Health Services Research, Department of Clinical Medicine, Aalborg University, 9220 Aalborg, Denmark
| | - Etheresia Pretorius
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa
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Kell DB, Khan MA, Kane B, Lip GYH, Pretorius E. Possible Role of Fibrinaloid Microclots in Postural Orthostatic Tachycardia Syndrome (POTS): Focus on Long COVID. J Pers Med 2024; 14:170. [PMID: 38392604 PMCID: PMC10890060 DOI: 10.3390/jpm14020170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024] Open
Abstract
Postural orthostatic tachycardia syndrome (POTS) is a common accompaniment of a variety of chronic, inflammatory diseases, including long COVID, as are small, insoluble, 'fibrinaloid' microclots. We here develop the argument, with accompanying evidence, that fibrinaloid microclots, through their ability to block the flow of blood through microcapillaries and thus cause tissue hypoxia, are not simply correlated with but in fact, by preceding it, may be a chief intermediary cause of POTS, in which tachycardia is simply the body's exaggerated 'physiological' response to hypoxia. Similar reasoning accounts for the symptoms bundled under the term 'fatigue'. Amyloids are known to be membrane disruptors, and when their targets are nerve membranes, this can explain neurotoxicity and hence the autonomic nervous system dysfunction that contributes to POTS. Taken together as a system view, we indicate that fibrinaloid microclots can serve to link POTS and fatigue in long COVID in a manner that is at once both mechanistic and explanatory. This has clear implications for the treatment of such diseases.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
- The Novo Nordisk Foundation Centre for Biosustainability, Building 220, Chemitorvet 200, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch Private Bag X1, Matieland 7602, South Africa
| | - Muhammed Asad Khan
- Directorate of Respiratory Medicine, Manchester University Hospitals, Wythenshawe Hospital, Manchester M23 9LT, UK
| | - Binita Kane
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
- Manchester University Foundation Trust and School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Gregory Y H Lip
- Liverpool Centre for Cardiovascular Science at University of Liverpool, Liverpool John Moores University and Liverpool Heart & Chest Hospital, Liverpool L14 3PE, UK
- Danish Center for Health Services Research, Department of Clinical Medicine, Aalborg University, 9220 Aalborg, Denmark
| | - Etheresia Pretorius
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch Private Bag X1, Matieland 7602, South Africa
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Pal I, Dey SG. The Role of Heme and Copper in Alzheimer's Disease and Type 2 Diabetes Mellitus. JACS AU 2023; 3:657-681. [PMID: 37006768 PMCID: PMC10052274 DOI: 10.1021/jacsau.2c00572] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 06/19/2023]
Abstract
Beyond the well-explored proposition of protein aggregation or amyloidosis as the central event in amyloidogenic diseases like Alzheimer's Disease (AD), and Type 2 Diabetes Mellitus (T2Dm); there are alternative hypotheses, now becoming increasingly evident, which suggest that the small biomolecules like redox noninnocent metals (Fe, Cu, Zn, etc.) and cofactors (Heme) have a definite influence in the onset and extent of such degenerative maladies. Dyshomeostasis of these components remains as one of the common features in both AD and T2Dm etiology. Recent advances in this course reveal that the metal/cofactor-peptide interactions and covalent binding can alarmingly enhance and modify the toxic reactivities, oxidize vital biomolecules, significantly contribute to the oxidative stress leading to cell apoptosis, and may precede the amyloid fibrils formation by altering their native folds. This perspective highlights this aspect of amyloidogenic pathology which revolves around the impact of the metals and cofactors in the pathogenic courses of AD and T2Dm including the active site environments, altered reactivities, and the probable mechanisms involving some highly reactive intermediates as well. It also discusses some in vitro metal chelation or heme sequestration strategies which might serve as a possible remedy. These findings might open up a new paradigm in our conventional understanding of amyloidogenic diseases. Moreover, the interaction of the active sites with small molecules elucidates potential biochemical reactivities that can inspire designing of drug candidates for such pathologies.
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Affiliation(s)
- Ishita Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick
Road, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick
Road, Jadavpur, Kolkata 700032, India
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Kalita S, Bergman H, Dubey KD, Shaik S. How Can Static and Oscillating Electric Fields Serve in Decomposing Alzheimer's and Other Senile Plaques? J Am Chem Soc 2023; 145:3543-3553. [PMID: 36735972 PMCID: PMC9936589 DOI: 10.1021/jacs.2c12305] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Alzheimer's disease is one of the most common neurodegenerative conditions, which are ascribed to extracellular accumulation of β-amyloid peptides into plaques. This phenomenon seems to typify other related neurodegenerative diseases. The present study uses classical molecular-dynamics simulations to decipher the aggregation-disintegration behavior of β-amyloid peptide plaques in the presence of static and oscillating oriented external electric fields (OEEFs). A long-term disintegration of such plaques is highly desirable since this may improve the prospects of therapeutic treatments of Alzheimer's disease and of other neurodegenerative diseases typified by senile plaques. Our study illustrates the spontaneous aggregation of the β-amyloid, its prevention and breakdown when OEEF is applied, and the fate of the broken aggregate when the OEEF is removed. Notably, we demonstrate that the usage of an oscillating OEEF on β-amyloid aggregates appears to lead to an irreversible disintegration. Insight is provided into the root causes of the various modes of aggregation, as well as into the different fates of OEEF-induced disintegration in oscillating vs static fields. Finally, our simulation results are compared to the well-established TTFields and the Deep Brain Stimulation (DBS) therapies, which are currently used options for treatments of Alzheimer's disease and other related neurodegenerative diseases.
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Affiliation(s)
- Surajit Kalita
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Hagai Bergman
- Department of Medical Neurobiology (Physiology), The Hebrew University of Jerusalem, Hadassah Medical Faculty, Jerusalem, Israel 91120
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh 201314, India
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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Nath AK, Roy M, Dey C, Dey A, Dey SG. Spin state dependent peroxidase activity of heme bound amyloid β peptides relevant to Alzheimer's disease. Chem Sci 2022; 13:14305-14319. [PMID: 36545147 PMCID: PMC9749105 DOI: 10.1039/d2sc05008k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022] Open
Abstract
The colocalization of heme rich deposits in the senile plaque of Aβ in the cerebral cortex of the Alzheimer's disease (AD) brain along with altered heme homeostasis and heme deficiency symptoms in AD patients has invoked the association of heme in AD pathology. Heme bound Aβ complexes, depending on the concentration of the complex or peptide to heme ratio, exhibit an equilibrium between a high-spin mono-His bound peroxidase-type active site and a low-spin bis-His bound cytochrome b type active site. The high-spin heme-Aβ complex shows higher peroxidase activity than free heme, where compound I is the reactive oxidant. It is also capable of oxidizing neurotransmitters like serotonin in the presence of peroxide, owing to the formation of compound I. The low-spin bis-His heme-Aβ complex on the other hand shows enhanced peroxidase activity relative to high-spin heme-Aβ. It reacts with H2O2 to produce two stable intermediates, compound 0 and compound I, which are characterized by absorption, EPR and resonance Raman spectroscopy. The stability of compound I of low-spin heme-Aβ is accountable for its enhanced peroxidase activity and oxidation of the neurotransmitter serotonin. The effect of the second sphere Tyr10 residue of Aβ on the formation and stability of the intermediates of low-spin heme-Aβ has also been investigated. The higher stability of compound I for low-spin heme-Aβ is likely due to H-bonding interactions involving Tyr10 in the distal pocket.
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Affiliation(s)
- Arnab Kumar Nath
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
| | - Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
| | - Chinmay Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science2A & 2B, Raja S. C. Mullick Road, JadavpurKolkata 700032India
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