1
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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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2
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He W, Kirmizialtin S. Mechanism of Cationic Lipid Induced DNA Condensation: Lipid-DNA Coordination and Divalent Cation Charge Fluctuations. Biomacromolecules 2024; 25:4819-4830. [PMID: 39011747 PMCID: PMC11323003 DOI: 10.1021/acs.biomac.4c00192] [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: 02/11/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024]
Abstract
The condensation of nucleic acids by lipids is a widespread phenomenon in biology with crucial implications for drug delivery. However, the mechanisms of DNA assembly in lipid bilayers remain insufficiently understood due to challenges in measuring and assessing each component's contribution in the lipid-DNA-cation system. This study uses all-atom molecular dynamics simulations to investigate DNA condensation in cationic lipid bilayers. Our exhaustive exploration of the thermodynamic factors reveals unique roles for phospholipid head groups and cations. We observed that bridging cations between lipid and DNA drastically reduce charges, while mobile magnesium cations "ping-ponging" between double strands create charge fluctuations. While the first factor stabilizes the DNA-lipid complex, the latter creates attractive forces to induce the spontaneous condensation of DNAs. This novel mechanism not only sheds light on the current data regarding cationic lipid-induced DNA condensation but also provides potential design strategies for creating efficient gene delivery vectors for drug delivery.
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Affiliation(s)
- Weiwei He
- Chemistry
Program, Science Division, New York University
Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Serdal Kirmizialtin
- Chemistry
Program, Science Division, New York University
Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department
of Chemistry, New York University, New York, New York 10003, United States
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3
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Skeens A, Markle JM, Petipas G, Frey SL, Legleiter J. Divalent cations promote huntingtin fibril formation on endoplasmic reticulum derived and model membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184339. [PMID: 38763270 DOI: 10.1016/j.bbamem.2024.184339] [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: 09/13/2023] [Revised: 04/24/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
Huntington's Disease (HD) is caused by an abnormal expansion of the polyglutamine (polyQ) domain within the first exon of the huntingtin protein (htt). This expansion promotes disease-related htt aggregation into amyloid fibrils and the formation of proteinaceous inclusion bodies within neurons. Fibril formation is a complex heterogenous process involving an array of aggregate species such as oligomers, protofibrils, and fibrils. In HD, structural abnormalities of membranes of several organelles develop. In particular, the accumulation of htt fibrils near the endoplasmic reticulum (ER) impinges upon the membrane, resulting in ER damage, altered dynamics, and leakage of Ca2+. Here, the aggregation of htt at a bilayer interface assembled from ER-derived liposomes was investigated, and fibril formation directly on these membranes was enhanced. Based on these observations, simplified model systems were used to investigate mechanisms associated with htt aggregation on ER membranes. As the ER-derived liposome fractions contained residual Ca2+, the role of divalent cations was also investigated. In the absence of lipids, divalent cations had minimal impact on htt structure and aggregation. However, the presence of Ca2+ or Mg2+ played a key role in promoting fibril formation on lipid membranes despite reduced htt insertion into and association with lipid interfaces, suggesting that the ability of divalent cations to promote fibril formation on membranes is mediated by induced changes to the lipid membrane physicochemical properties. With enhanced concentrations of intracellular calcium being a hallmark of HD, the ability of divalent cations to influence htt aggregation at lipid membranes may play a role in aggregation events that lead to organelle abnormalities associated with disease.
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Affiliation(s)
- Adam Skeens
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, USA
| | - Jordyn M Markle
- The Department of Chemistry, Gettysburg College, 300 N. Washington Street, Gettysburg, PA 17325, USA
| | - Gabriella Petipas
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, USA
| | - Shelli L Frey
- The Department of Chemistry, Gettysburg College, 300 N. Washington Street, Gettysburg, PA 17325, USA.
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, USA; Rockefeller Neurosciences Institutes, West Virginia University, 1 Medical Center Dr., P.O. Box 9303, Morgantown, WV 26505, USA; Department of Neuroscience, West Virginia University, 1 Medical Center Dr., P.O. Box 9303, Morgantown, WV 26505, USA.
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4
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Kaygisiz K, Rauch-Wirth L, Dutta A, Yu X, Nagata Y, Bereau T, Münch J, Synatschke CV, Weil T. Data-mining unveils structure-property-activity correlation of viral infectivity enhancing self-assembling peptides. Nat Commun 2023; 14:5121. [PMID: 37612273 PMCID: PMC10447463 DOI: 10.1038/s41467-023-40663-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
Gene therapy via retroviral vectors holds great promise for treating a variety of serious diseases. It requires the use of additives to boost infectivity. Amyloid-like peptide nanofibers (PNFs) were shown to efficiently enhance retroviral gene transfer. However, the underlying mode of action of these peptides remains largely unknown. Data-mining is an efficient method to systematically study structure-function relationship and unveil patterns in a database. This data-mining study elucidates the multi-scale structure-property-activity relationship of transduction enhancing peptides for retroviral gene transfer. In contrast to previous reports, we find that not the amyloid fibrils themselves, but rather µm-sized β-sheet rich aggregates enhance infectivity. Specifically, microscopic aggregation of β-sheet rich amyloid structures with a hydrophobic surface pattern and positive surface charge are identified as key material properties. We validate the reliability of the amphiphilic sequence pattern and the general applicability of the key properties by rationally creating new active sequences and identifying short amyloidal peptides from various pathogenic and functional origin. Data-mining-even for small datasets-enables the development of new efficient retroviral transduction enhancers and provides important insights into the diverse bioactivity of the functional material class of amyloids.
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Affiliation(s)
- Kübra Kaygisiz
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Lena Rauch-Wirth
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstraße 1, 89081, Ulm, Germany
| | - Arghya Dutta
- Department Polymer Theory, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Xiaoqing Yu
- Department Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Yuki Nagata
- Department Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tristan Bereau
- Department Polymer Theory, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstraße 1, 89081, Ulm, Germany
| | - Christopher V Synatschke
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
| | - Tanja Weil
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
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5
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Chowdhury UD, Paul A, Bhargava BL. Interaction of the tau fibrils with the neuronal membrane. Biophys Chem 2023; 298:107024. [PMID: 37104971 DOI: 10.1016/j.bpc.2023.107024] [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: 03/03/2023] [Revised: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023]
Abstract
Tau proteins are recently gaining a lot of interest due to their active role in causing a range of tauopathies. Molecular mechanisms underlying the tau interaction with the neuronal membrane are hitherto unknown and difficult to characterize using experimental methods. Using the cryo-EM structure of the tau-fibrils we have used atomistic molecular dynamics simulation to model the tau fibril and neuronal membrane interaction using explicit solvation. The dynamics and structural characteristics of the tau fibril with the neuronal membrane are compared to the tau fibril in the aqueous phase to corroborate the effect of the neuronal membrane in the tau structure. Tau fibrils have been modelled using CHARMM-36m force field and the six component neuronal membrane composition is taken from the earlier simulation results. The timescale conceivable in our molecular dynamics simulations is of the order of microseconds which captures the onset of the interaction of the tau fibrils with the neuronal membrane. This interaction is found to impact the tau pathogenesis that finally causes neuronal toxicity. Our study initiates the understanding of tau conformational ensemble in the presence of neuronal membrane and sheds the light on the significant tau-membrane interactions.
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Affiliation(s)
- Unmesh D Chowdhury
- School of Chemical Sciences, National Institute of Science Education & Research-Bhubaneswar, An OCC of Homi Bhabha National Institute, P.O. Jatni, Khurda, Odisha 752050, India
| | - Arnav Paul
- School of Chemical Sciences, National Institute of Science Education & Research-Bhubaneswar, An OCC of Homi Bhabha National Institute, P.O. Jatni, Khurda, Odisha 752050, India
| | - B L Bhargava
- School of Chemical Sciences, National Institute of Science Education & Research-Bhubaneswar, An OCC of Homi Bhabha National Institute, P.O. Jatni, Khurda, Odisha 752050, India.
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6
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John T, Piantavigna S, Dealey TJA, Abel B, Risselada HJ, Martin LL. Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism. Chem Sci 2023; 14:3730-3741. [PMID: 37035708 PMCID: PMC10074436 DOI: 10.1039/d3sc00159h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
The self-assembly of peptides into supramolecular structures has been linked to neurodegenerative diseases but has also been observed in functional roles. Peptides are physiologically exposed to crowded environments of biomacromolecules, and particularly cellular membrane lipids. Previous research has shown that membranes can both accelerate and inhibit peptide self-assembly. Here, we studied the impact of membrane models that mimic cellular oxidative stress and compared this to mammalian and bacterial membranes. Using molecular dynamics simulations and experiments, we propose a model that explains how changes in peptide-membrane binding, electrostatics, and peptide secondary structure stabilization determine the nature of peptide self-assembly. We explored the influence of zwitterionic (POPC), anionic (POPG) and oxidized (PazePC) phospholipids, as well as cholesterol, and mixtures thereof, on the self-assembly kinetics of the amyloid β (1-40) peptide (Aβ40), linked to Alzheimer's disease, and the amyloid-forming antimicrobial peptide uperin 3.5 (U3.5). We show that the presence of an oxidized lipid had similar effects on peptide self-assembly as the bacterial mimetic membrane. While Aβ40 fibril formation was accelerated, U3.5 aggregation was inhibited by the same lipids at the same peptide-to-lipid ratio. We attribute these findings and peptide-specific effects to differences in peptide-membrane adsorption with U3.5 being more strongly bound to the membrane surface and stabilized in an α-helical conformation compared to Aβ40. Different peptide-to-lipid ratios resulted in different effects. We found that electrostatic interactions are a primary driving force for peptide-membrane interaction, enabling us to propose a model for predicting how cellular changes might impact peptide self-assembly in vivo.
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Affiliation(s)
- Torsten John
- School of Chemistry, Monash University Clayton VIC 3800 Australia
- Leibniz Institute of Surface Engineering (IOM) Permoserstraße 15 04318 Leipzig Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Institute of Chemical Technology, Leipzig University Linnéstraße 3 04103 Leipzig Germany
| | | | - Tiara J A Dealey
- School of Chemistry, Monash University Clayton VIC 3800 Australia
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM) Permoserstraße 15 04318 Leipzig Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Institute of Chemical Technology, Leipzig University Linnéstraße 3 04103 Leipzig Germany
| | - Herre Jelger Risselada
- Leibniz Institute of Surface Engineering (IOM) Permoserstraße 15 04318 Leipzig Germany
- Institute for Theoretical Physics, Georg-August-Universität Göttingen Friedrich-Hund-Platz 1 37077 Göttingen Germany
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7
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Qi Z, Wan M, Zhang J, Li Z. Influence of Cholesterol on the Membrane Binding and Conformation of α-Synuclein. J Phys Chem B 2023; 127:1956-1964. [PMID: 36812386 DOI: 10.1021/acs.jpcb.2c08077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The α-Synuclein (α-Syn) plays an important role in the pathology of Parkinson's disease (PD), and its oligomers and fibrils are toxic to the nervous system. As organisms age, the cholesterol content in biological membranes increases, which is a potential cause of PD. Cholesterol may affect the membrane binding of α-Syn and its abnormal aggregation, but the mechanism remains unclear. Here, we present our molecular dynamics simulation studies on the interaction between α-Syn and lipid membranes, with or without cholesterol. It is demonstrated that cholesterol provides additional hydrogen bond interaction with α-Syn; however, the coulomb interaction and hydrophobic interaction between α-Syn and lipid membranes could be weakened by cholesterol. In addition, cholesterol leads to the shrinking of lipid packing defects and the decrease of lipid fluidity, thereby shortening the membrane binding region of α-Syn. Under these multifaceted effects of cholesterol, membrane-bound α-Syn shows signs of forming a β-sheet structure, which may further induce the formation of abnormal α-Syn fibrils. These results provide important information for the understanding of membrane binding of α-Syn, and they are expected to promote the bridging between cholesterol and the pathological aggregation of α-Syn.
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Affiliation(s)
- Ziqiang Qi
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Menglin Wan
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Jun Zhang
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Zhen Li
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
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8
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Tiwari A, Pradhan S, Sannigrahi A, Mahakud AK, Jha S, Chattopadhyay K, Biswas M, Saleem M. “Interplay of lipid-head group and packing defects in driving Amyloid-beta mediated myelin-like model membrane deformation”. J Biol Chem 2023; 299:104653. [PMID: 36990217 PMCID: PMC10148160 DOI: 10.1016/j.jbc.2023.104653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/24/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Accumulating evidence suggests that amyloid plaque associated myelin lipid loss as a result of elevated amyloid burden might also contribute to Alzheimer's disease. The amyloid fibrils though closely associated with lipids under physiological conditions, however, the progression of membrane remodeling events leading to lipid-fibril assembly remains unknown. Here we first reconstitute the interaction of Aβ-40 with myelin-like model membrane and show that the binding of Aβ-40 induces extensive tubulation. To look into the mechanism of membrane tubulation we chose a set of membrane conditions varying in lipid packing density and net charge that allows us to dissect the contribution of lipid specificity of Aβ-40 binding, aggregation kinetics, and subsequent changes in membrane parameters such as fluidity, diffusion, and compressibility modulus. We show that the binding of Aβ-40 depends predominantly on the lipid packing defect densities and electrostatic interactions and results in rigidification of the myelin-like model membrane during the early phase of amyloid aggregation. Furthermore, elongation of Aβ-40 into higher oligomeric and fibrillar species leads to eventual fluidization of the model membrane followed by extensive lipid membrane tubulation observed in the late phase. Taken together, our results capture mechanistic insights into snapshots of temporal dynamics of Aβ-40 - myelin-like model membrane interaction and demonstrate how short timescale, local phenomena of binding, and fibril-mediated load generation results in the consequent association of lipids with growing amyloid fibrils.
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9
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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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10
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Adélaïde M, Salnikov E, Ramos-Martín F, Aisenbrey C, Sarazin C, Bechinger B, D’Amelio N. The Mechanism of Action of SAAP-148 Antimicrobial Peptide as Studied with NMR and Molecular Dynamics Simulations. Pharmaceutics 2023; 15:pharmaceutics15030761. [PMID: 36986623 PMCID: PMC10051583 DOI: 10.3390/pharmaceutics15030761] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
Background: SAAP-148 is an antimicrobial peptide derived from LL-37. It exhibits excellent activity against drug-resistant bacteria and biofilms while resisting degradation in physiological conditions. Despite its optimal pharmacological properties, its mechanism of action at the molecular level has not been explored. Methods: The structural properties of SAAP-148 and its interaction with phospholipid membranes mimicking mammalian and bacterial cells were studied using liquid and solid-state NMR spectroscopy as well as molecular dynamics simulations. Results: SAAP-148 is partially structured in solution and stabilizes its helical conformation when interacting with DPC micelles. The orientation of the helix within the micelles was defined by paramagnetic relaxation enhancements and found similar to that obtained using solid-state NMR, where the tilt and pitch angles were determined based on 15N chemical shift in oriented models of bacterial membranes (POPE/POPG). Molecular dynamic simulations revealed that SAAP-148 approaches the bacterial membrane by forming salt bridges between lysine and arginine residues and lipid phosphate groups while interacting minimally with mammalian models containing POPC and cholesterol. Conclusions: SAAP-148 stabilizes its helical fold onto bacterial-like membranes, placing its helix axis almost perpendicular to the surface normal, thus probably acting by a carpet-like mechanism on the bacterial membrane rather than forming well-defined pores.
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Affiliation(s)
- Morgane Adélaïde
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France
| | - Evgeniy Salnikov
- Institut de Chimie, UMR7177, Université de Strasbourg/CNRS, 67000 Strasbourg, France
| | - Francisco Ramos-Martín
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France
- Correspondence: (F.R.-M.); (N.D.); Tel.: +33-3-22-82-74-73 (F.R.-M. & N.D.)
| | - Christopher Aisenbrey
- Institut de Chimie, UMR7177, Université de Strasbourg/CNRS, 67000 Strasbourg, France
| | - Catherine Sarazin
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France
| | - Burkhard Bechinger
- Institut de Chimie, UMR7177, Université de Strasbourg/CNRS, 67000 Strasbourg, France
| | - Nicola D’Amelio
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France
- Correspondence: (F.R.-M.); (N.D.); Tel.: +33-3-22-82-74-73 (F.R.-M. & N.D.)
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11
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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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12
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Aksenova AY, Likhachev IV, Grishin SY, Galzitskaya OV. The Increased Amyloidogenicity of Spike RBD and pH-Dependent Binding to ACE2 May Contribute to the Transmissibility and Pathogenic Properties of SARS-CoV-2 Omicron as Suggested by In Silico Study. Int J Mol Sci 2022; 23:13502. [PMID: 36362302 PMCID: PMC9655063 DOI: 10.3390/ijms232113502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/19/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
SARS-CoV-2 is a rapidly evolving pathogen that has caused a global pandemic characterized by several consecutive waves. Based on epidemiological and NGS data, many different variants of SARS-CoV-2 were described and characterized since the original variant emerged in Wuhan in 2019. Notably, SARS-CoV-2 variants differ in transmissibility and pathogenicity in the human population, although the molecular basis for this difference is still debatable. A significant role is attributed to amino acid changes in the binding surface of the Spike protein to the ACE2 receptor, which may facilitate virus entry into the cell or contribute to immune evasion. We modeled in silico the interaction between Spike RBDs of Wuhan-Hu-1, Delta, and Omicron BA.1 variants and ACE2 at different pHs (pH 5 and pH 7) and showed that the strength of this interaction was higher for the Omicron BA.1 RBD compared to Wuhan-Hu-1 or Delta RBDs and that the effect was more profound at pH 5. This finding is strikingly related to the increased ability of Omicron variants to spread in the population. We also noted that during its spread in the population, SARS-CoV-2 evolved to a more charged, basic composition. We hypothesize that the more basic surface of the Omicron variant may facilitate its spread in the upper respiratory tract but not in the lower respiratory tract, where pH estimates are different. We calculated the amyloidogenic properties of Spike RBDs in different SARS-CoV-2 variants and found eight amyloidogenic regions in the Spike RBDs for each of the variants predicted by the FoldAmyloid program. Although all eight regions were almost identical in the Wuhan to Gamma variants, two of them were significantly longer in both Omicron variants, making the Omicron RBD more amyloidogenic. We discuss how the increased predicted amyloidogenicity of the Omicron variants RBDs may be important for protein stability, influence its interaction with ACE2 and contribute to immune evasion.
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Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Ilya V. Likhachev
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Mathematical Problems of Biology RAS, The Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Sergei Y. Grishin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
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13
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Pham T, Cheng KH. Exploring the binding kinetics and behaviors of self-aggregated beta-amyloid oligomers to phase-separated lipid rafts with or without ganglioside-clusters. Biophys Chem 2022; 290:106874. [PMID: 36067650 DOI: 10.1016/j.bpc.2022.106874] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/25/2022] [Accepted: 08/03/2022] [Indexed: 11/21/2022]
Abstract
Lipid binding kinetics and energetics of self-aggregated and disordered beta-amyloid oligomers of various sizes, from solution to lipid raft surfaces, were investigated using MD simulations. Our systems include small (monomers to tetramers) and larger (octamers and dodecamers) oligomers. Our lipid rafts contain saturated and unsaturated phosphatidylcholine (PC), cholesterol, and with or without asymmetrically distributed monosialotetrahexosylganglioside (GM1). All rafts exhibited dynamic and structurally diversified domains including liquid-ordered (Lo), liquid-disordered (Ld), and interfacial Lod domains. For rafts without GM1, all oligomers bound to the Lod domain. For GM1-containing rafts, all small oligomers and most larger oligomers bound specifically to the GM1-clusters embedded in the Lo domain. Lipid-protein binding energies followed an order of GM1 >> unsaturated PC > saturated PC > cholesterol for all rafts. In addition, protein-induced membrane structural disruption increased progressively with the size of the oligomer for the annular lipids surrounding the membrane-bound protein in non-GM1-containing rafts. We propose that the tight binding of beta-amyloid oligomers to the GM1-clusters and the structural perturbation of lipids surrounding the membrane-bound proteins at the Lod domain are early molecular events of the beta-amyloid aggregation process on neuronal membrane surfaces that trigger the onset of Alzheimer's.
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Affiliation(s)
- Thuong Pham
- Department of Physics, Trinity University, United States of America
| | - Kwan H Cheng
- Department of Physics, Trinity University, United States of America; Department of Neuroscience, Trinity University, United States of America.
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14
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Yang Y, Distaffen H, Jalali S, Nieuwkoop AJ, Nilsson BL, Dias CL. Atomic Insights into Amyloid-Induced Membrane Damage. ACS Chem Neurosci 2022; 13:2766-2777. [PMID: 36095304 DOI: 10.1021/acschemneuro.2c00446] [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] [Indexed: 01/20/2023] Open
Abstract
Amphipathic peptides can cause biological membranes to leak either by dissolving their lipid content via a detergent-like mechanism or by forming pores on the membrane surface. These modes of membrane damage have been related to the toxicity of amyloid peptides and to the activity of antimicrobial peptides. Here, we perform the first all-atom simulations in which membrane-bound amphipathic peptides self-assemble into β-sheets that subsequently either form stable pores inside the bilayer or drag lipids out of the membrane surface. An analysis of these simulations shows that the acyl tail of lipids interact strongly with non-polar side chains of peptides deposited on the membrane. These strong interactions enable lipids to be dragged out of the bilayer by oligomeric structures accounting for detergent-like damage. They also disturb the orientation of lipid tails in the vicinity of peptides. These distortions are minimized around pore structures. We also show that membrane-bound β-sheets become twisted with one of their extremities partially penetrating the lipid bilayer. This allows peptides on opposite leaflets to interact and form a long transmembrane β-sheet, which initiates poration. In simulations, where peptides are deposited on a single leaflet, the twist in β-sheets allows them to penetrate the membrane and form pores. In addition, our simulations show that fibril-like structures produce little damage to lipid membranes, as non-polar side chains in these structures are unavailable to interact with the acyl tail of lipids.
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Affiliation(s)
- Yanxing Yang
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Hannah Distaffen
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Andrew J Nieuwkoop
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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15
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Kenyaga JM, Cheng Q, Qiang W. Early-Stage β-Amyloid-Membrane Interactions Modulate Lipid Dynamics and Influence Structural Interfaces and Fibrillation. J Biol Chem 2022; 298:102491. [PMID: 36115457 PMCID: PMC9556791 DOI: 10.1016/j.jbc.2022.102491] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 11/02/2022] Open
Abstract
Molecular interactions between β-amyloid (Aβ) peptide and membranes contribute to the neuronal toxicity of Aβ and the pathology of Alzheimer's disease (AD). Neuronal plasma membranes serve as biologically relevant environments for the Aβ aggregation process as well as affect the structural polymorphisms of Aβ aggregates. However, the nature of these interactions is unknown. Here, we utilized solid-state NMR spectroscopy to explore the site-specific interactions between Aβ peptides and lipids in synaptic plasma membranes at the membrane-associated nucleation stage. The key results show that different segments in the hydrophobic sequence of Aβ initiate membrane binding and inter-strand assembling. We demonstrate early-stage Aβ-lipid interactions modulate lipid dynamics, leading to more rapid lipid headgroup motion and reduced lateral diffusive motion. These early events influence the structural polymorphisms of yielded membrane-associated Aβ fibrils with distinct C-terminal quaternary interface structure compared to fibrils grown in aqueous solutions. Based on our results, we propose a schematic mechanism by which Aβ-lipid interactions drive membrane-associated nucleation processes, providing molecular insights into the early events of fibrillation in biological environments.
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Affiliation(s)
- June M Kenyaga
- Department of Chemistry, Binghamton University, the State University of New York
| | - Qinghui Cheng
- Department of Chemistry, Binghamton University, the State University of New York
| | - Wei Qiang
- Department of Chemistry, Binghamton University, the State University of New York.
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16
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Chowdhury UD, Paul A, Bhargava BL. The effect of lipid composition on the dynamics of tau fibrils. Proteins 2022; 90:2103-2115. [DOI: 10.1002/prot.26401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/01/2022] [Accepted: 07/15/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Unmesh Dutta Chowdhury
- School of Chemical Sciences National Institute of Science Education & Research‐Bhubaneswar, OCC of Homi Bhabha National Institute Khurda Odisha India
| | - Arnav Paul
- School of Chemical Sciences National Institute of Science Education & Research‐Bhubaneswar, OCC of Homi Bhabha National Institute Khurda Odisha India
| | - B. L. Bhargava
- School of Chemical Sciences National Institute of Science Education & Research‐Bhubaneswar, OCC of Homi Bhabha National Institute Khurda Odisha India
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17
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Antila HS, Kav B, Miettinen MS, Martinez-Seara H, Jungwirth P, Ollila OHS. Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks. J Phys Chem B 2022. [DOI: 10.1021/acs.jpcb.2c01954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hanne S. Antila
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Batuhan Kav
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum
Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany
| | - Markus S. Miettinen
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
- Department of Chemistry, University of Bergen, 5020 Bergen, Norway
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - O. H. Samuli Ollila
- Institute of Biotechonology, University of Helsinki, Helsinki 00014, Finland
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18
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Geng Y, Huang T, Zhou W, Shen L. Physical Mechanism of Amyloid-β Peptide Chain Aggregation on Fluidic Lipid Nanotubules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5752-5758. [PMID: 35476922 DOI: 10.1021/acs.langmuir.2c00357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The question of how peptide chain aggregation is influenced by lipid membranes with varying shapes and structures is crucial for a detailed understanding of the neurotoxicity effect of the peptide chains. Not like the more usual spherical liposomes and planar lipid membranes, herein, we use lipid nanotubules as a model of important neuron synapse nanowire structures and devote particular attention to the effect of nanotubule fluidity on amyloid-β peptide (Aβ) chain aggregation. We apply single-molecule tracking (SMT) to elucidate how Aβ chains diffuse and aggregate on lipid nanotubules with different fluidities. The physical mechanism implies that fluidic lipid nanotubules facilitate the super-diffusion of two-dimensional (2D)-mobile precursor Aβ chains and promote their aggregation. This aggregation mechanism is retarded on less fluidic lipid nanotubules where the super-diffusion of 2D-mobile precursor Aβ chains is restricted by "frozen" lipids with less mobility. This work provides a mechanistic explanation for Aβ chain aggregation on fluidic lipid nanotubules.
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19
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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