1
|
The contribution of individual residues of an aggregative hexapeptide derived from the human γD-crystallin to its amyloidogenicity. Int J Biol Macromol 2022; 201:182-192. [PMID: 34998884 DOI: 10.1016/j.ijbiomac.2021.12.192] [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: 10/25/2021] [Revised: 12/22/2021] [Accepted: 12/30/2021] [Indexed: 11/24/2022]
Abstract
Human γD-crystallin protein is abundant in the lens and is essential for preserving lens transparency. With age the protein may lose its native structure resulting in the formation of cataract. We recently reported an aggregative peptide, 41Gly-Cys-Trp-Met-Leu-Tyr46 from the human γD-crystallin, termed GDC6, exhibiting amyloidogenic properties in vitro. Here, we aimed to determine the contribution of each residue of the GDC6 to its amyloidogenicity. Molecular dynamic (MD) simulations revealed that the residues Trp, Leu, and Tyr played an important role in the amyloidogenicity of GDC6 by facilitating inter-peptide main-chain hydrogen bonds, and π-π interactions. MD predictions were further validated using single-, double- and triple-alanine-substituted GDC6 peptides in which their amyloidogenic propensity was individually evaluated using complementary biophysical techniques including Thioflavin T assay, turbidity assay, CD spectroscopy, and TEM imaging. Results revealed that the substitution of Trp, Leu, and Tyr together by Ala completely abolished aggregation of GDC6 in vitro, highlighting their importance in the amyloidogenicity of GDC6.
Collapse
|
2
|
Hung NB, Le DM, Hoang TX. Sequence dependent aggregation of peptides and fibril formation. J Chem Phys 2018; 147:105102. [PMID: 28915764 DOI: 10.1063/1.5001517] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides. Fibril-like ordered aggregates are found for several sequences that contain the common HPH pattern, while other sequences may form helix bundles or disordered aggregates. A wide variation of the aggregation transition temperatures among sequences, even among those of the same hydrophobic fraction, indicates that not all sequences undergo aggregation at a presumable physiological temperature. The transition is found to be the most cooperative for sequences forming fibril-like structures. For a fibril-prone sequence, it is shown that fibril formation follows the nucleation and growth mechanism. Interestingly, a binary mixture of peptides of an aggregation-prone and a non-aggregation-prone sequence shows the association and conversion of the latter to the fibrillar structure. Our study highlights the role of a sequence in selecting fibril-like aggregates and also the impact of a structural template on fibril formation by peptides of unrelated sequences.
Collapse
Affiliation(s)
- Nguyen Ba Hung
- Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan, Ba Dinh, Hanoi, Vietnam
| | - Duy-Manh Le
- Institute of Research and Development, Duy Tan University, K7/25 Quang Trung, Da Nang, Vietnam
| | - Trinh X Hoang
- Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan, Ba Dinh, Hanoi, Vietnam
| |
Collapse
|
3
|
Dudukovic NA, Hudson BC, Paravastu AK, Zukoski CF. Self-assembly pathways and polymorphism in peptide-based nanostructures. NANOSCALE 2018; 10:1508-1516. [PMID: 29303206 DOI: 10.1039/c7nr06724k] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Dipeptide derivative molecules can self-assemble into space-filling nanofiber networks at low volume fractions (<1%), allowing the formation of molecular gels with tunable mechanical properties. The self-assembly of dipeptide-based molecules is reminiscent of pathological amyloid fibril formation by naturally occurring polypeptides. Fluorenylmethoxycarbonyl-diphenylalanine (Fmoc-FF) is the most widely studied such molecule, but the thermodynamic and kinetic phenomena giving rise to Fmoc-FF gel formation remain poorly understood. We have previously presented evidence that the gelation process is a first order phase transition characterized by low energy barriers to nucleation, short induction times, and rapid quasi-one-dimensional crystal growth, stemming from solvent-solute interactions and highly specific molecular packing. Here, we discuss the phase behavior of Fmoc-FF in different solvents. We find that Fmoc-FF gel formation can be induced in apolar solvents, in addition to previously established pathways in aqueous systems. We further show that in certain solvent systems anisotropic crystals (nanofibers) are an initial metastable state, after which macroscopic crystal aggregates with no preferred axis of growth are formed. The molecular conformation is sensitive to solvent composition during assembly, indicating that Fmoc-FF may be a simple model system to study complex thermodynamic and kinetic phenomena involved in peptide self-assembly.
Collapse
Affiliation(s)
- Nikola A Dudukovic
- Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551, USA.
| | | | | | | |
Collapse
|
4
|
Auer S. Simple Model of the Effect of Solution Conditions on the Nucleation of Amyloid Fibrils. J Phys Chem B 2017; 121:8893-8901. [DOI: 10.1021/acs.jpcb.7b05400] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefan Auer
- School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
| |
Collapse
|
5
|
Abstract
We present a theoretical model for the nucleation of amyloid fibrils. In our model we use helix-coil theory to describe the equilibrium between a soluble native state and an aggregation-prone unfolded state. We then extend the theory to include oligomers with β-sheet cores and calculate the free energy of these states using estimates for the energies of H-bonds, steric zipper interactions, and the conformational entropy cost of forming secondary structure. We find that states with fewer than ~10 β-strands are unstable relative to the dissociated state and three β-strands is the highest free energy state. We then use a modified version of Classical Nucleation Theory to compute the nucleation rate of fibrils from a supersaturated solution of monomers, dimers, and trimers. The nucleation rate has a non-monotonic dependence on denaturant concentration reflecting the competing effects of destabilizing the fibril and increasing the concentration of unfolded monomers. We estimate heterogeneous nucleation rates and discuss the application of our model to secondary nucleation.
Collapse
Affiliation(s)
- Lingyun Zhang
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
| |
Collapse
|
6
|
An B, Wu X, Li M, Chen Y, Li F, Yan X, Wang J, Li C, Brennan C. Hydrophobicity-modulating self-assembled morphologies of α-zein in aqueous ethanol. Int J Food Sci Technol 2016. [DOI: 10.1111/ijfs.13248] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Baozhen An
- CAS Key Laboratory of Bio-based Materials; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Songling Road 189 Qingdao 266101 China
- Bioengineering Department; College of Chemical Engineering; Qingdao University of Science & Technology; Zhengzhou Road 53 Qingdao 266042 China
| | - Xiaochen Wu
- CAS Key Laboratory of Bio-based Materials; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Songling Road 189 Qingdao 266101 China
| | - Mingjie Li
- CAS Key Laboratory of Bio-based Materials; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Songling Road 189 Qingdao 266101 China
| | - Yijun Chen
- CAS Key Laboratory of Bio-based Materials; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Songling Road 189 Qingdao 266101 China
- College of Textiles and Fashion; Qingdao University; Ningxia Road 308 Qingdao 266071 China
| | - Fei Li
- CAS Key Laboratory of Bio-based Materials; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Songling Road 189 Qingdao 266101 China
| | - Xiaofei Yan
- CAS Key Laboratory of Bio-based Materials; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Songling Road 189 Qingdao 266101 China
| | - Jialin Wang
- Bioengineering Department; College of Chemical Engineering; Qingdao University of Science & Technology; Zhengzhou Road 53 Qingdao 266042 China
| | - Chaoxu Li
- CAS Key Laboratory of Bio-based Materials; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Songling Road 189 Qingdao 266101 China
| | - Charles Brennan
- Department of Wine, Food and Molecular Biosciences; Lincoln University; Lincoln 7647 New Zealand
| |
Collapse
|
7
|
Kashchiev D. Protein Polymerization into Fibrils from the Viewpoint of Nucleation Theory. Biophys J 2016; 109:2126-36. [PMID: 26588571 DOI: 10.1016/j.bpj.2015.10.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/30/2015] [Accepted: 10/02/2015] [Indexed: 01/08/2023] Open
Abstract
The assembly of various proteins into fibrillar aggregates is an important phenomenon with wide implications ranging from human disease to nanoscience. Using general kinetic results of nucleation theory, we analyze the polymerization of protein into linear or helical fibrils in the framework of the Oosawa-Kasai (OK) model. We show that while within the original OK model of linear polymerization the process does not involve nucleation, within a modified OK model it is nucleation-mediated. Expressions are derived for the size of the fibril nucleus, the work for fibril formation, the nucleation barrier, the equilibrium and stationary fibril size distributions, and the stationary fibril nucleation rate. Under otherwise equal conditions, this rate decreases considerably when the short (subnucleus) fibrils lose monomers much more frequently than the long (supernucleus) fibrils, a feature that should be born in mind when designing a strategy for stymying or stimulating fibril nucleation. The obtained dependence of the nucleation rate on the concentration of monomeric protein is convenient for experimental verification and for use in rate equations accounting for nucleation-mediated fibril formation. The analysis and the results obtained for linear fibrils are fully applicable to helical fibrils whose formation is describable by a simplified OK model.
Collapse
Affiliation(s)
- Dimo Kashchiev
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| |
Collapse
|
8
|
Irbäck A, Wessén J. Thermodynamics of amyloid formation and the role of intersheet interactions. J Chem Phys 2016; 143:105104. [PMID: 26374063 DOI: 10.1063/1.4930280] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The self-assembly of proteins into β-sheet-rich amyloid fibrils has been observed to occur with sigmoidal kinetics, indicating that the system initially is trapped in a metastable state. Here, we use a minimal lattice-based model to explore the thermodynamic forces driving amyloid formation in a finite canonical (NVT) system. By means of generalized-ensemble Monte Carlo techniques and a semi-analytical method, the thermodynamic properties of this model are investigated for different sets of intersheet interaction parameters. When the interactions support lateral growth into multi-layered fibrillar structures, an evaporation/condensation transition is observed, between a supersaturated solution state and a thermodynamically distinct state where small and large fibril-like species exist in equilibrium. Intermediate-size aggregates are statistically suppressed. These properties do not hold if aggregate growth is one-dimensional.
Collapse
Affiliation(s)
- Anders Irbäck
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Jonas Wessén
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| |
Collapse
|
9
|
Zou Y, Sun Y, Zhu Y, Ma B, Nussinov R, Zhang Q. Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein. ACS Chem Neurosci 2016; 7:286-96. [PMID: 26815332 PMCID: PMC7842942 DOI: 10.1021/acschemneuro.5b00242] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aggregation of the copper-zinc superoxide dismutase (SOD1) protein is linked to familial amyotrophic lateral sclerosis, a progressive neurodegenerative disease. A recent experimental study has shown that the (147)GVIGIAQ(153) SOD1 C-terminal segment not only forms amyloid fibrils in isolation but also accelerates the aggregation of full-length SOD1, while substitution of isoleucine at site 149 by proline blocks its fibril formation. Amyloid formation is a nucleation-polymerization process. In this study, we investigated the oligomerization and the nucleus structure of this heptapeptide. By performing extensive replica-exchange molecular dynamics (REMD) simulations and conventional MD simulations, we found that the GVIGIAQ hexamers can adopt highly ordered bilayer β-sheets and β-barrels. In contrast, substitution of I149 by proline significantly reduces the β-sheet probability and results in the disappearance of bilayer β-sheet structures and the increase of disordered hexamers. We identified mixed parallel-antiparallel bilayer β-sheets in both REMD and conventional MD simulations and provided the conformational transition from the experimentally observed parallel bilayer sheets to the mixed parallel-antiparallel bilayer β-sheets. Our simulations suggest that the critical nucleus consists of six peptide chains and two additional peptide chains strongly stabilize this critical nucleus. The stabilized octamer is able to recruit additional random peptides into the β-sheet. Therefore, our simulations provide insights into the critical nucleus formation and the smallest stable nucleus of the (147)GVIGIAQ(153) peptide.
Collapse
Affiliation(s)
- Yu Zou
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, China
| | - Yunxiang Sun
- Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Yuzhen Zhu
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, China
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, China
| |
Collapse
|
10
|
Nucleation of polymorphic amyloid fibrils. Biophys J 2016; 108:1176-86. [PMID: 25762329 DOI: 10.1016/j.bpj.2015.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 01/09/2015] [Accepted: 01/13/2015] [Indexed: 11/23/2022] Open
Abstract
One and the same protein can self-assemble into amyloid fibrils with different morphologies. The phenomenon of fibril polymorphism is relevant biologically because different fibril polymorphs can have different toxicity, but there is no tool for predicting which polymorph forms and under what conditions. Here, we consider the nucleation of polymorphic amyloid fibrils occurring by direct polymerization of monomeric proteins into fibrils. We treat this process within the framework of our newly developed nonstandard nucleation theory, which allows prediction of the concentration dependence of the nucleation rate for different fibril polymorphs. The results highlight that the concentration dependence of the nucleation rate is closely linked with the protein solubility and a threshold monomer concentration below which fibril formation becomes biologically irrelevant. The relation between the nucleation rate, the fibril solubility, the threshold concentration, and the binding energies of the fibril building blocks within fibrils might prove a valuable tool for designing new experiments to control the formation of particular fibril polymorphs.
Collapse
|
11
|
Abstract
It is well established that amyloid fibril solubility is protein specific, but how solubility depends on the interactions between the fibril building blocks is not clear. Here we use a simple protein model and perform Monte Carlo simulations to directly measure the solubility of amyloid fibrils as a function of the interaction between the fibril building blocks. Our simulations confirms that the fibril solubility depends on the fibril thickness and that the relationship between the interactions and the solubility can be described by a simple analytical formula. The results presented in this study reveal general rules how side-chain-side-chain interactions, backbone hydrogen bonding, and temperature affect amyloid fibril solubility, which might prove to be a powerful tool to design protein fibrils with desired solubility and aggregation properties in general.
Collapse
Affiliation(s)
- L G Rizzi
- School of Chemistry, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - S Auer
- School of Chemistry, University of Leeds , Leeds LS2 9JT, United Kingdom
| |
Collapse
|
12
|
Phillips JC. Thermodynamic description of Beta amyloid formation using physicochemical scales and fractal bioinformatic scales. ACS Chem Neurosci 2015; 6:745-50. [PMID: 25702750 DOI: 10.1021/cn5001793] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Protein function depends on both protein structure and amino acid (aa) sequence. Here we show that modular features of both structure and function can be quantified economically from the aa sequences alone for the small (40,42 aa) plaque-forming (aggregative) amyloid beta fragments. Some edge and center features of the fragments are predicted. Bioinformatic scales based on β strand formation propensities and the thermodynamically second order fractal hydropathicity scale based on evolutionary optimization (self-organized criticality) are contrasted with the standard first order physicochemical scale based on complete protein (water-air) unfolding. The results are consistent with previous studies of these physicochemical factors that show that aggregative properties, even of beta fragments, are driven primarily by near-equilibrium hydropathic forces.
Collapse
Affiliation(s)
- J. C. Phillips
- Department
of Physics and
Astronomy, Rutgers University, Piscataway, New Jersey 08854, United States
| |
Collapse
|
13
|
Abraham JN, Kedracki D, Prado E, Gourmel C, Maroni P, Nardin C. Effect of the Interaction of the amyloid β (1-42) peptide with short single-stranded synthetic nucleotide sequences: morphological characterization of the inhibition of fibrils formation and fibrils disassembly. Biomacromolecules 2014; 15:3253-8. [PMID: 25093956 DOI: 10.1021/bm501004q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The formation of extracellular neuritic plaques in the brain of individuals who suffered from Alzheimer's disease (AD) is a major pathological hallmark. These plaques consist of filamentous aggregates of the amyloid beta (1-42) (Aβ42) proteins. Prevention or reduction of the formation of these fibrils is foreseen as a potential therapeutic approach. In this context, we investigated the interactions between the Aβ42 protein and polyions, in particular short single stranded synthetic nucleotide sequences. The experimental outcomes reported herein provide evidence of the inhibition of amyloid fibril genesis as well as disassembly of existing fibers through electrostatic interaction between the Aβ42 protein and the polyions. Since the polyions and the Aβ42 protein are oppositely charged, the formation of (micellar) inter polyelectrolyte complexes (IPECs) is likely to occur. Since the abnormal deposition of amyloid fibers is an archetype of AD, the outcomes of these investigations, supported by atomic force microscopy imaging in the dry and liquid states, as well as circular dichroism and Fourier transform infrared spectroscopy, are of high interest for the development of future strategies to cure a disease that concerns an ever aging population.
Collapse
Affiliation(s)
- Jancy Nixon Abraham
- Faculty of Sciences, Department of Inorganic and Analytical Chemistry, University of Geneva , Quai Ernest Ansermet 30, CH-1211, Geneva 4, Switzerland
| | | | | | | | | | | |
Collapse
|