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Chen Z, Xiao X, Yang L, Lian C, Xu S, Liu H. Prion-like Aggregation of the Heptapeptide GNNQQNY into Amyloid Nanofiber Is Governed by Configuration Entropy. J Chem Inf Model 2023; 63:6423-6435. [PMID: 37782627 DOI: 10.1021/acs.jcim.3c00370] [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: 10/04/2023]
Abstract
A major cause of prion infectivity is the early formation of small, fibril-like aggregates consisting of the heptapeptide GNNQQNY. The prion aggregates exhibit a unique stacking mode in which the hydrophobic tyrosine (Y) is exposed outward, forming a bilayer β-sheet-stacking zipper structure. This stacking mode of the prion peptides, termed "Y-outward" structure for convenience, goes against the common understanding that, for other amyloid-forming peptides, the hydrophobic residues should be hidden within the peptide fibril, referred to as "Y-inward" structure. To explore the extraordinary stacking behaviors of the prion GNNQQNY peptides, two fibril models are constructed in a fashion of "Y-outward" and "Y-inward" stackings and then studied in silico to examine their thermodynamic stabilities and disaggregation pathways. The "Y-inward" structure indeed exhibits stronger thermodynamic stability than the "Y-outward" structure, according to potential energy and stacking energy calculations. To show how the peptide fibrils dissociate, we illustrated two disaggregation pathways. A dihedral-based free energy landscape was then calculated to examine the conformational degrees of freedom of the GNNQQNY chains in the "Y-outward" and "Y-inward" structures. Peptide chains lose more configurational entropy in the "Y-inward" structure than in the "Y-outward" structure, indicating that the prion peptides are prone to aggregate in a fashion of "Y-outward" stacking pattern due to its low conformational constraints. The prion-like aggregation of the GNNQQNY peptides into amyloid fibrils is primarily governed by the configuration entropy.
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Affiliation(s)
- Zhangyang Chen
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xingqing Xiao
- Department of Chemistry, School of Chemistry and Chemical Engineering, Hainan University, Haikou City, Hainan Province 570228, P. R. China
| | - Li Yang
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Cheng Lian
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Shouhong Xu
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Honglai Liu
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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Ermakova E, Makshakova O, Kurbanov R, Ibraev I, Zuev Y, Sedov I. Aggregation of Amyloidogenic Peptide Uperin-Molecular Dynamics Simulations. Molecules 2023; 28:molecules28104070. [PMID: 37241811 DOI: 10.3390/molecules28104070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Uperin 3.5 is a remarkable natural peptide obtained from the skin of toadlets comprised of 17 amino acids which exhibits both antimicrobial and amyloidogenic properties. Molecular dynamics simulations were performed to study the β-aggregation process of uperin 3.5 as well as two of its mutants, in which the positively charged residues Arg7 and Lys8 have been replaced by alanine. All three peptides rapidly underwent spontaneous aggregation and conformational transition from random coils to beta-rich structures. The simulations reveal that the initial and essential step of the aggregation process involves peptide dimerization and the formation of small beta-sheets. A decrease in positive charge and an increase in the number of hydrophobic residues in the mutant peptides lead to an increase in the rate of their aggregation.
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Affiliation(s)
- Elena Ermakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
| | - Olga Makshakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
| | - Rauf Kurbanov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
| | - Ilya Ibraev
- Chemical Institute, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Yuriy Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
| | - Igor Sedov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
- Chemical Institute, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
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Veloso SRS, Tiryaki E, Spuch C, Hilliou L, Amorim CO, Amaral VS, Coutinho PJG, Ferreira PMT, Salgueiriño V, Correa-Duarte MA, Castanheira EMS. Tuning the drug multimodal release through a co-assembly strategy based on magnetic gels. NANOSCALE 2022; 14:5488-5500. [PMID: 35332904 DOI: 10.1039/d1nr08158f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Self-assembled short peptide-based gels are highly promising drug delivery systems. However, implementing a stimulus often requires screening different structures to obtain gels with suitable properties, and drugs might not be well encapsulated and/or cause undesirable effects on the gel's properties. To overcome this challenge, a new design approach is presented to modulate the release of doxorubicin as a model chemotherapeutic drug through the interplay of (di)phenylalanine-coated magnetic nanoparticles, PEGylated liposomes and doxorubicin co-assembly in dehydropeptide-based gels. The composites enable an enhancement of the gelation kinetics in a concentration-dependent manner, mainly through the use of PEGylated liposomes. The effect of the co-assembly of phenylalanine-coated nanoparticles with the hydrogel displays a concentration and size dependence. Finally, the integration of liposomes as doxorubicin storage units and of nanoparticles as composites that co-assemble with the gel matrix enables the tuneability of both passive and active doxorubicin release through a thermal, and a low-frequency alternating magnetic field-based trigger. In addition to the modulation of the gel properties, the functionalization with (di)phenylalanine improves the cytocompatibility of the nanoparticles. Hereby, this work paves a way for the development of peptide-based supramolecular systems for on-demand and controlled release of drugs.
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Affiliation(s)
- Sérgio R S Veloso
- Physics Centre of Minho and Porto Universities (CF-UM-UP) and LaPMET (Laboratory of Physics for Materials and Emergent Technologies), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Ecem Tiryaki
- Departamento de Física Aplicada, Universidade de Vigo, 36310 Vigo, Spain
| | - Carlos Spuch
- Translational Neuroscience Research Group, Galicia Sur Health Research Institute, CIBERSAM, Hospital Álvaro Cunqueiro, Bloque Técnico, Planta 2, Sala de Investigación, Estrada Clara Campoamor, 341, 36212 Vigo, Spain
| | - Loic Hilliou
- Institute for Polymers and Composites, Department of Polymer Engineering, University of Minho, Campus de Azurém, 4800-058 Guimarães, Portugal
| | - C O Amorim
- Physics Department and CICECO, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - V S Amaral
- Physics Department and CICECO, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Paulo J G Coutinho
- Physics Centre of Minho and Porto Universities (CF-UM-UP) and LaPMET (Laboratory of Physics for Materials and Emergent Technologies), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Paula M T Ferreira
- Centro de Química (CQUM), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Verónica Salgueiriño
- Departamento de Física Aplicada, Universidade de Vigo, 36310 Vigo, Spain
- CINBIO, Universidad de Vigo, 36310 Vigo, Spain.
| | | | - Elisabete M S Castanheira
- Physics Centre of Minho and Porto Universities (CF-UM-UP) and LaPMET (Laboratory of Physics for Materials and Emergent Technologies), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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Kong H, Liu B, Yang G, Chen Y, Wei G. Tailoring Peptide Self-Assembly and Formation of 2D Nanoribbons on Mica and HOPG Surface. MATERIALS 2022; 15:ma15010310. [PMID: 35009456 PMCID: PMC8745981 DOI: 10.3390/ma15010310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 12/10/2022]
Abstract
Studying the interactions between biomolecules and material interfaces play a crucial role in the designing and synthesizing of functional bionanomaterials with tailored structure and function. Previously, a lot of studies were performed on the self-assembly of peptides in solution through internal and external stimulations, which mediated the creation of peptide nanostructures from zero-dimension to three-dimension. In this study, we demonstrate the self-assembly behavior of the GNNQQNY peptide on the surface of mica and highly oriented pyrolytic graphite through tailoring the self-assembly conditions. Various factors, such as the type of dissolvent, peptide concentration, pH value, and evaporation period on the formation of peptide nanofibers and nanoribbons with single- and bi-directional arrays are investigated. It is found that the creation of peptide nanoribbons on both mica and HOPG can be achieved effectively through adjusting and optimizing the experimental parameters. Based on the obtained results, the self-assembly and formation mechanisms of peptide nanoribbons on both material interfaces are discussed. It is expected that the findings obtained in this study will inspire the design of motif-specific peptides with high binding affinity towards materials and mediate the green synthesis of peptide-based bionanomaterials with unique function and application potential.
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Affiliation(s)
| | | | | | | | - Gang Wei
- Correspondence: ; Tel.: +86-150-6624-2101
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Burra G, Maina MB, Serpell LC, Thakur AK. Nucleation-dependent Aggregation Kinetics of Yeast Sup35 Fragment GNNQQNY. J Mol Biol 2020; 433:166732. [PMID: 33279578 DOI: 10.1016/j.jmb.2020.166732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
An N-terminal hepta-peptide sequence of yeast prion protein Sup35 with the sequence GNNQQNY is widely used as a model system for amyloid fibril formation. In this study, we used a reproducible solubilisation protocol that allows the generation of a homogenous monomeric solution of GNNQQNY to uncover the molecular details of its self-assembly mechanism. The aggregation kinetics data show that the GNNQQNY sequence follows nucleation-dependent aggregation kinetics with a critical nucleus of size ~7 monomers and that the efficiency of nucleation were found to be inversely related to the reaction temperature. The nucleus reduces the thermodynamic energy barrier by acting as a template for further self-assembly and results in highly ordered amyloid fibrils. The fibers grown at different temperatures showed similar Thioflavin T fluorescence, Congo-red binding and β-sheet rich structures displaying a characteristic cross-β diffraction pattern. These aggregates also share morphological and structural identity with those reported earlier. The mature GNNQQNY fibers did not exert significant oxidative stress or cytotoxicity upon incubating with differentiated SHSY5Y cells. To our knowledge, this is the first study to experimentally validate previous nucleus size predictions based on theoretical and molecular dynamics simulations. These findings provide the basis for understanding the kinetics and thermodynamics of amyloid nucleation and elongation of amyloidogenic proteins/peptides associated with many systemic and neurodegenerative diseases.
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Affiliation(s)
- Gunasekhar Burra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, India; Sussex Neuroscience, School of Life Sciences, University of Sussex, UK.
| | - Mahmoud B Maina
- Sussex Neuroscience, School of Life Sciences, University of Sussex, UK; College of Medical Sciences, Yobe State University, Nigeria
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, UK
| | - Ashwani K Thakur
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, India.
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