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Rangubpit W, Sungted S, Wong-Ekkabut J, Distaffen HE, Nilsson BL, Dias CL. Pore Formation by Amyloid-like Peptides: Effects of the Nonpolar-Polar Sequence Pattern. ACS Chem Neurosci 2024; 15:3354-3362. [PMID: 39172951 DOI: 10.1021/acschemneuro.4c00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024] Open
Abstract
One of the mechanisms accounting for the toxicity of amyloid peptides in diseases like Alzheimer's and Parkinson's is the formation of pores on the plasma membrane of neurons. Here, we perform unbiased all-atom simulations of the full membrane damaging pathway, which includes adsorption, aggregation, and perforation of the lipid bilayer accounting for pore-like structures. Simulations are performed using four peptides made with the same amino acids. Differences in the nonpolar-polar sequence pattern of these peptides prompt them to adsorb into the membrane with the extended conformations oriented either parallel [peptide labeled F1, Ac-(FKFE)2-NH2], perpendicular (F4, Ac-FFFFKKEE-NH2), or with an intermediate orientation (F2, Ac-FFKKFFEE-NH2, and F3, Ac-FFFKFEKE-NH2) in regard to the membrane surface. At the water-lipid interface, only F1 fully self-assembles into β-sheets, and F2 peptides partially fold into an α-helical structure. The β-sheets of F1 emerge as electrostatic interactions attract neighboring peptides to intermediate distances where nonpolar side chains can interact within the dry core of the bilayer. This complex interplay between electrostatic and nonpolar interactions is not observed for the other peptides. Although β-sheets of F1 peptides are mostly parallel to the membrane, some of their edges penetrate deep inside the bilayer, dragging water molecules with them. This precedes pore formation, which starts with the flow of two water layers through the membrane that expand into a stable cylindrical pore delimited by polar faces of β-sheets spanning both leaflets of the bilayer.
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Affiliation(s)
- Warin Rangubpit
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Siwaporn Sungted
- Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Jirasak Wong-Ekkabut
- Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Hannah E Distaffen
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
- Materials Science Program, University of Rochester, Rochester, New York 14627-0166, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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Tang Y, Zhang Y, Zhang D, Liu Y, Nussinov R, Zheng J. Exploring pathological link between antimicrobial and amyloid peptides. Chem Soc Rev 2024; 53:8713-8763. [PMID: 39041297 DOI: 10.1039/d3cs00878a] [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: 07/24/2024]
Abstract
Amyloid peptides (AMYs) and antimicrobial peptides (AMPs) are considered as the two distinct families of peptides, characterized by their unique sequences, structures, biological functions, and specific pathological targets. However, accumulating evidence has revealed intriguing pathological connections between these peptide families in the context of microbial infection and neurodegenerative diseases. Some AMYs and AMPs share certain structural and functional characteristics, including the ability to self-assemble, the presence of β-sheet-rich structures, and membrane-disrupting mechanisms. These shared features enable AMYs to possess antimicrobial activity and AMPs to acquire amyloidogenic properties. Despite limited studies on AMYs-AMPs systems, the cross-seeding phenomenon between AMYs and AMPs has emerged as a crucial factor in the bidirectional communication between the pathogenesis of neurodegenerative diseases and host defense against microbial infections. In this review, we examine recent developments in the potential interplay between AMYs and AMPs, as well as their pathological implications for both infectious and neurodegenerative diseases. By discussing the current progress and challenges in this emerging field, this account aims to inspire further research and investments to enhance our understanding of the intricate molecular crosstalk between AMYs and AMPs. This knowledge holds great promise for the development of innovative therapies to combat both microbial infections and neurodegenerative disorders.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio 44325, USA.
| | - Yanxian Zhang
- Division of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Dong Zhang
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
- Department of Human Molecular Genetics and Biochemistry Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio 44325, USA.
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Fan X, Zhang X, Yan J, Xu H, Zhao W, Ding F, Huang F, Sun Y. Computational Investigation of Coaggregation and Cross-Seeding between Aβ and hIAPP Underpinning the Cross-Talk in Alzheimer's Disease and Type 2 Diabetes. J Chem Inf Model 2024; 64:5303-5316. [PMID: 38921060 PMCID: PMC11339732 DOI: 10.1021/acs.jcim.4c00859] [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: 06/27/2024]
Abstract
The coexistence of amyloid-β (Aβ) and human islet amyloid polypeptide (hIAPP) in the brain and pancreas is associated with an increased risk of Alzheimer's disease (AD) and type 2 diabetes (T2D) due to their coaggregation and cross-seeding. Despite this, the molecular mechanisms underlying their interaction remain elusive. Here, we systematically investigated the cross-talk between Aβ and hIAPP using atomistic discrete molecular dynamics (DMD) simulations. Our results revealed that the amyloidogenic core regions of both Aβ (Aβ10-21 and Aβ30-41) and hIAPP (hIAPP8-20 and hIAPP22-29), driving their self-aggregation, also exhibited a strong tendency for cross-interaction. This propensity led to the formation of β-sheet-rich heterocomplexes, including potentially toxic β-barrel oligomers. The formation of Aβ and hIAPP heteroaggregates did not impede the recruitment of additional peptides to grow into larger aggregates. Our cross-seeding simulations demonstrated that both Aβ and hIAPP fibrils could mutually act as seeds, assisting each other's monomers in converting into β-sheets at the exposed fibril elongation ends. The amyloidogenic core regions of Aβ and hIAPP, in both oligomeric and fibrillar states, exhibited the ability to recruit isolated peptides, thereby extending the β-sheet edges, with limited sensitivity to the amino acid sequence. These findings suggest that targeting these regions by capping them with amyloid-resistant peptide drugs may hold potential as a therapeutic approach for addressing AD, T2D, and their copathologies.
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Affiliation(s)
- Xinjie Fan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
| | - Xiaohan Zhang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Jiajia Yan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
| | - Huan Xu
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Wenhui Zhao
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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Huang F, Fan X, Wang Y, Zou Y, Lian J, Wang C, Ding F, Sun Y. Computational insights into the cross-talk between medin and Aβ: implications for age-related vascular risk factors in Alzheimer's disease. Brief Bioinform 2024; 25:bbad526. [PMID: 38271485 PMCID: PMC10810335 DOI: 10.1093/bib/bbad526] [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: 11/08/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
The aggregation of medin forming aortic medial amyloid is linked to arterial wall degeneration and cerebrovascular dysfunction. Elevated levels of arteriolar medin are correlated with an increased presence of vascular amyloid-β (Aβ) aggregates, a hallmark of Alzheimer's disease (AD) and vascular dementia. The cross-interaction between medin and Aβ results in the formation of heterologous fibrils through co-aggregation and cross-seeding processes both in vitro and in vivo. However, a comprehensive molecular understanding of the cross-interaction between medin and Aβ-two intrinsically disordered proteins-is critically lacking. Here, we employed atomistic discrete molecular dynamics simulations to systematically investigate the self-association, co-aggregation and also the phenomenon of cross-seeding between these two proteins. Our results demonstrated that both Aβ and medin were aggregation prone and their mixture tended to form β-sheet-rich hetero-aggregates. The formation of Aβ-medin hetero-aggregates did not hinder Aβ and medin from recruiting additional Aβ and medin peptides to grow into larger β-sheet-rich aggregates. The β-barrel oligomer intermediates observed in the self-aggregations of Aβ and medin were also present during their co-aggregation. In cross-seeding simulations, preformed Aβ fibrils could recruit isolated medin monomers to form elongated β-sheets. Overall, our comprehensive simulations suggested that the cross-interaction between Aβ and medin may contribute to their pathological aggregation, given the inherent amyloidogenic tendencies of both medin and Aβ. Targeting medin, therefore, could offer a novel therapeutic approach to preserving brain function during aging and AD by improving vascular health.
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Affiliation(s)
- Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
| | - Xinjie Fan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Ying Wang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yu Zou
- Department of Sport and Exercise Science, Zhejiang University, Hangzhou 310058, China
| | - Jiangfang Lian
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
| | - Chuang Wang
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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Huang F, Liu Y, Wang Y, Xu J, Lian J, Zou Y, Wang C, Ding F, Sun Y. Co-aggregation of α-synuclein with amyloid-β stabilizes β-sheet-rich oligomers and enhances the formation of β-barrels. Phys Chem Chem Phys 2023; 25:31604-31614. [PMID: 37964757 DOI: 10.1039/d3cp04138g] [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: 11/16/2023]
Abstract
Alzheimer's disease (AD) and Parkinson's disease (PD) are the two most common neurodegenerative diseases with markedly different pathological features of β-amyloid (Aβ) plaques and α-synuclein (αS) Lewy bodies (LBs), respectively. However, clinical overlaps in symptoms and pathologies between AD and PD are commonly observed caused by the cross-interaction between Aβ and αS. To uncover the molecular mechanisms behind their overlapping symptoms and pathologies, we computationally investigated the impact of αS on an Aβ monomer and dimerization using atomistic discrete molecular dynamics simulations (DMD). Our results revealed that αS could directly interact with Aβ monomers and dimers, thus forming β-sheet-rich oligomers, including potentially toxic β-barrel intermediates. The binding hotspot involved the second half of the N-terminal domain and NAC region in αS, along with residues 10-21 and 31-42 in Aβ. In their hetero-complex, the binding hotspot primarily assumed a β-sheet core buried inside, which was dynamically shielded by the highly charged, amyloid-resistant C-terminus of αS. Because the amyloid prion region was the same as the binding hotspot being buried, their fibrillization may be delayed, causing the toxic oligomers to increase. This study sheds light on the intricate relationship between Aβ and αS and provides insights into the overlapping pathology of AD and PD.
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Affiliation(s)
- Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
| | - Yuying Liu
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.
| | - Ying Wang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.
| | - Jia Xu
- School of Medicine, Ningbo University, Ningbo 315211, China.
| | - Jiangfang Lian
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
| | - Yu Zou
- Department of Sport and Exercise Science, Zhejiang University, Hangzhou 310058, China
| | - Chuang Wang
- School of Medicine, Ningbo University, Ningbo 315211, China.
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
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Maurer M, Lazaridis T. Transmembrane β-Barrel Models of α-Synuclein Oligomers. J Chem Inf Model 2023; 63:7171-7179. [PMID: 37963823 DOI: 10.1021/acs.jcim.3c00997] [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: 11/16/2023]
Abstract
The aggregation of α-synuclein is implicated in a number of neurodegenerative diseases, such as Parkinson's and Multiple System Atrophy, but the role of these aggregates in disease development is not clear. One possible mechanism of cytotoxicity is the disturbance or permeabilization of cell membranes by certain types of oligomers. However, no high-resolution structure of such membrane-embedded complexes has ever been determined. Here we construct and evaluate putative transmembrane β-barrels formed by this protein. Examination of the α-synuclein sequence reveals two regions that could form membrane-embedded β-hairpins: 64-92 (the NAC), and 35-56, which harbors many familial Parkinson's mutations. The stability of β-barrels formed by these hairpins is examined first in implicit membrane pores and then by multimicrosecond all-atom simulations. We find that a NAC region barrel remains stably inserted and hydrated for at least 10 μs. A 35-56 barrel remains stably inserted in the membrane but dehydrates and collapses if all His50 are neutral or if His50 is replaced by Q. If half of the His50 are doubly protonated, the barrel takes an oval shape but remains hydrated for at least 10 μs. Possible implications of these findings for α-synuclein pathology are discussed.
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Affiliation(s)
- Manuela Maurer
- Department of Chemistry & Biochemistry, City College of New York/CUNY, 160 Convent Ave, New York, New York 10031, United States
| | - Themis Lazaridis
- Department of Chemistry & Biochemistry, City College of New York/CUNY, 160 Convent Ave, New York, New York 10031, United States
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Ma L, Li X, Petersen RB, Peng A, Huang K. Probing the interactions between amyloidogenic proteins and bio-membranes. Biophys Chem 2023; 296:106984. [PMID: 36889133 DOI: 10.1016/j.bpc.2023.106984] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/11/2023] [Accepted: 02/22/2023] [Indexed: 03/01/2023]
Abstract
Protein misfolding diseases (PMDs) in humans are characterized by the deposition of protein aggregates in tissues, including Alzheimer's disease, Parkinson's disease, type 2 diabetes, and amyotrophic lateral sclerosis. Misfolding and aggregation of amyloidogenic proteins play a central role in the onset and progression of PMDs, and these processes are regulated by multiple factors, especially the interaction between proteins and bio-membranes. Bio-membranes induce conformational changes in amyloidogenic proteins and affect their aggregation; on the other hand, the aggregates of amyloidogenic proteins may cause membrane damage or dysfunction leading to cytotoxicity. In this review, we summarize the factors that affect the binding of amyloidogenic proteins and membranes, the effects of bio-membranes on the aggregation of amyloidogenic proteins, mechanisms of membrane disruption by amyloidogenic aggregates, technical approaches for detecting these interactions, and finally therapeutic strategies targeting membrane damage caused by amyloidogenic proteins.
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Affiliation(s)
- Liang Ma
- Department of Pharmacy, Wuhan Mental Health Center, Wuhan, China; Department of Pharmacy, Wuhan Hospital for Psychotherapy, Wuhan, China
| | - Xi Li
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Robert B Petersen
- Foundational Sciences, Central Michigan University College of Medicine, Mount Pleasant, MI, USA
| | - Anlin Peng
- Department of Pharmacy, The Third Hospital of Wuhan, Tongren Hospital of Wuhan University, Wuhan, China.
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Abstract
An understanding of how the amino acid sequence affects the interaction of peptides with lipid membranes remains mostly unknown. This type of knowledge is required to rationalize membrane-induced toxicity of amyloid peptides and to design peptides that can interact with lipid bilayers. Here, we perform a systematic study of how variations in the sequence of the amphipathic Ac-(FKFE)2-NH2 peptide affect its interaction with zwitterionic lipid bilayers using extensive all-atom molecular dynamics simulations in explicit solvent. Our results show that peptides with a net positive charge bind more frequently to the lipid bilayer than neutral or negatively charged sequences. Moreover, neutral amphipathic peptides made with the same numbers of phenylalanine (F), lysine (K), and glutamic (E) amino acids at different positions in the sequence differ significantly in their frequency of binding to the membrane. We find that peptides bind with a higher frequency to the membrane if their positive lysine side chains are more exposed to the solvent, which occurs if they are located at the extremity (as opposed to the middle) of the sequence. Non-polar residues play an important role in accounting for the adsorption of peptides onto the membrane. In particular, peptides made with less hydrophobic non-polar residues (e.g., valine and alanine) are significantly less adsorbed to the membrane compared to peptides made with phenylalanine. We also find that sequences where phenylalanine residues are located at the extremities of the peptide have a higher tendency to be adsorbed.
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Affiliation(s)
- Yanxing Yang
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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