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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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Kumar A, Mishra B, Konar AD, Mylonakis E, Basu A. Molecular Dynamics Simulations Help Determine the Molecular Mechanisms of Lasioglossin-III and Its Variant Peptides' Membrane Interfacial Interactions. J Phys Chem B 2024; 128:6049-6058. [PMID: 38840325 DOI: 10.1021/acs.jpcb.4c02387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Lasioglossin-III (LL-III) is a potent broad-spectrum antimicrobial peptide used in diverse antimicrobial applications. In this work, coarse-grained and all-atom molecular dynamics simulation strategies were used in tandem to interpret the molecular mechanisms involved in the interfacial dynamics of LL-III and its recombinant variants during interactions with diverse cell membrane systems. Our results indicate that the membrane charges act as the driving force for initiating the membrane-peptide interactions, while the hydrophobic or van der Waals forces help to reinforce the membrane-peptide bindings. The optimized charge-hydrophobicity ratio of the LL-III peptides helps ensure their high specificity toward bacterial membranes compared to mammalian membrane systems, which also helps explain our experimental observations. Overall, we hope that our work gives new insight into the antimicrobial action of LL-III peptides and that the adopted simulation strategy will help other scientists and engineers extract maximal information from complex molecular simulations using minimal computational power.
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Affiliation(s)
- Atul Kumar
- School of Pharmaceutical Sciences, Rajiv Gandhi Technological University, Airport Bypass Road, Gandhinagar, Bhopal 462033, India
| | - Biswajit Mishra
- Department of Medicine, Houston Methodist Hospital, Houston, Texas 77030, United States
| | - Anita Dutt Konar
- School of Pharmaceutical Sciences, Rajiv Gandhi Technological University, Airport Bypass Road, Gandhinagar, Bhopal 462033, India
- Department of Applied Chemistry, Rajiv Gandhi Technological University, Bhopal 462033, India
| | - Eleftherios Mylonakis
- Department of Medicine, Houston Methodist Hospital, Houston, Texas 77030, United States
| | - Anindya Basu
- School of Pharmaceutical Sciences, Rajiv Gandhi Technological University, Airport Bypass Road, Gandhinagar, Bhopal 462033, India
- School of Biomolecular Engineering and Biotechnology, Rajiv Gandhi Technological University, Bhopal 462033, India
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Nandi S, Sarkar N. Interactions between Lipid Vesicle Membranes and Single Amino Acid Fibrils: Probable Origin of Specific Neurological Disorders. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1971-1987. [PMID: 38240221 DOI: 10.1021/acs.langmuir.3c02429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Amyloid fibrils are known to be responsible for several neurological disorders, like Alzheimer's disease (AD), Parkinson's disease (PD), etc. For decades, mostly proteins and peptide-based amyloid fibrils have been focused on, and the topic has acknowledged the rise, development, understanding of, and controversy, as well. However, the single amino acid based amyloid fibrils, responsible for several disorders, such as phenylketonuria, tyrosenimia type II, hypermethioninemia, etc., have gotten scientific attention lately. To understand the molecular level pathogenesis of such disorders originated due to the accumulation of single amino acid-based amyloid fibrils, interaction of these fibrils with phospholipid vesicle membranes is found to be an excellent cell-free in vitro setup. Based on such an in vitro setup, these fibrils show a generic mechanism of membrane insertion driven by electrostatic and hydrophobic effects inside the membrane that reduces the integral rigidity of the membrane. Alteration of such fundamental properties of the membrane, therefore, might be referred to as one of the prime pathological factors for the development of these neurological disorders. Hence, such interactions must be investigated in cellular and intracellular compartments to design suitable therapeutic modulators against fibrils.
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Affiliation(s)
- Sourav Nandi
- Yale School of Medicine, Yale University, New Haven, Connecticut 06510, United States
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur, 721302, West Bengal, India
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Putri RA, Rohman MS, Swasono RT, Raharjo TJ. A novel synthetic peptide analog enhanced antibacterial activity of the frog-derived skin peptide wuchuanin-A1. J Biomol Struct Dyn 2023:1-11. [PMID: 37968993 DOI: 10.1080/07391102.2023.2281633] [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: 09/05/2023] [Accepted: 11/04/2023] [Indexed: 11/17/2023]
Abstract
In recent years, there has been a growing focus on the development of novel antibacterial compounds for clinical applications, such as antimicrobial peptide (AMP). Among the developed AMP, wuchuanin-A1, a coil-shaped bioactive peptide derived from Odorrana wuchuanensis frog skin, has been reported to exhibit antibacterial, antifungal, and antioxidant activity, but there are limited studies on its potential as an antibacterial agent. Therefore, this study aims to molecularly modify the sequence of wuchuanin-A1 to enhance its antibacterial properties. The interaction of both the native and analog peptide with bacterial inner membranes was initially assessed using computational methods. Specific amino acid substitutions were then used to enhance the modified peptide's antibacterial efficacy, followed by several preliminary tests to evaluate its activity. This study bridges the gap in exploring the potential of wuchuanin-A1 for antibacterial purposes, providing insights into the design of effective antimicrobial agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | - Tri Joko Raharjo
- Department of Chemistry, Universitas Gadjah Mada, Bulaksumur, Indonesia
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Trejos M, Aristizabal Y, Aragón-Muriel A, Oñate-Garzón J, Liscano Y. Characterization and Classification In Silico of Peptides with Dual Activity (Antimicrobial and Wound Healing). Int J Mol Sci 2023; 24:13091. [PMID: 37685896 PMCID: PMC10487549 DOI: 10.3390/ijms241713091] [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: 07/21/2023] [Revised: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
The growing challenge of chronic wounds and antibiotic resistance has spotlighted the potential of dual-function peptides (antimicrobial and wound healing) as novel therapeutic strategies. The investigation aimed to characterize and correlate in silico the physicochemical attributes of these peptides with their biological activity. We sourced a dataset of 207 such peptides from various peptide databases, followed by a detailed analysis of their physicochemical properties using bioinformatic tools. Utilizing statistical tools like clustering, correlation, and principal component analysis (PCA), patterns and relationships were discerned among these properties. Furthermore, we analyzed the peptides' functional domains for insights into their potential mechanisms of action. Our findings spotlight peptides in Cluster 2 as efficacious in wound healing, whereas Cluster 1 peptides exhibited pronounced antimicrobial potential. In our study, we identified specific amino acid patterns and peptide families associated with their biological activities, such as the cecropin antimicrobial domain. Additionally, we found the presence of polar amino acids like arginine, cysteine, and lysine, as well as apolar amino acids like glycine, isoleucine, and leucine. These characteristics are crucial for interactions with bacterial membranes and receptors involved in migration, proliferation, angiogenesis, and immunomodulation. While this study provides a groundwork for therapeutic development, translating these findings into practical applications necessitates additional experimental and clinical research.
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Affiliation(s)
- María Trejos
- Grupo de Investigación en Salud Integral (GISI), Departamento Facultad de Salud, Universidad Santiago de Cali, Cali 760035, Colombia;
| | - Yesid Aristizabal
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760035, Colombia; (Y.A.); (J.O.-G.)
| | - Alberto Aragón-Muriel
- Laboratorio de Investigación en Catálisis y Procesos (LICAP), Departamento de Química, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Cali 760001, Colombia;
- Grupo de Investigación e Innovación en Biotecnología (BITI), Tecnoparque Nodo Valle, Servicio Nacional de Aprendizaje (SENA), Cali 760044, Colombia
| | - José Oñate-Garzón
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760035, Colombia; (Y.A.); (J.O.-G.)
| | - Yamil Liscano
- Grupo de Investigación en Salud Integral (GISI), Departamento Facultad de Salud, Universidad Santiago de Cali, Cali 760035, Colombia;
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