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Kapuganti SK, Saumya KU, Verma D, Giri R. Investigating the aggregation perspective of Dengue virus proteome. Virology 2023; 586:12-22. [PMID: 37473502 DOI: 10.1016/j.virol.2023.07.010] [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] [Received: 04/24/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
Dengue viruses are human pathogens that are transmitted through mosquitoes. Apart from the typical symptoms associated with viral fevers, DENV infections are known to cause several neurological complications such as meningitis, encephalitis, intracranial haemorrhage, retinopathies along with the more severe, and sometimes fatal, vascular leakage and dengue shock syndrome. This study was designed to investigate, in detail, the predicted viral protein aggregation prone regions among all serotypes. Further, in order to understand the cross-talk between viral protein aggregation and aggregation of cellular proteins, cross-seeding experiments between the DENV NS1 (1-30), corresponding to the β-roll domain and the diabetes hallmark protein, amylin, were performed. Various techniques such as fluorescence spectroscopy, circular dichroism, atomic force microscopy and immunoblotting have been employed for this. We observe that the DENV proteomes have many predicted APRs and the NS1 (1-30) of DENV1-3, 2K and capsid anchor of DENV2 and DENV4 are capable of forming amyloids, in vitro. Further, the DENV NS1 (1-30), aggregates are also able to cross-seed and enhance amylin aggregation and vice-versa. This knowledge may lead to an opportunity for designing suitable inhibitors of protein aggregation that may be beneficial for viral infections and comorbidities.
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Affiliation(s)
- Shivani Krishna Kapuganti
- Indian Institute of Technology Mandi, School of Basic Sciences, VPO Kamand, Himachal Pradesh, 175005, India
| | - Kumar Udit Saumya
- Indian Institute of Technology Mandi, School of Basic Sciences, VPO Kamand, Himachal Pradesh, 175005, India
| | - Deepanshu Verma
- Indian Institute of Technology Mandi, School of Basic Sciences, VPO Kamand, Himachal Pradesh, 175005, India
| | - Rajanish Giri
- Indian Institute of Technology Mandi, School of Basic Sciences, VPO Kamand, Himachal Pradesh, 175005, India.
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Dec R, Okoń R, Puławski W, Wacławska M, Dzwolak W. Forced amyloidogenic cooperativity of structurally incompatible peptide segments: Fibrillization behavior of highly aggregation-prone A-chain fragment of insulin coupled to all-L, and alternating L/D octaglutamates. Int J Biol Macromol 2022; 223:362-369. [PMID: 36368353 DOI: 10.1016/j.ijbiomac.2022.11.050] [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: 10/26/2022] [Accepted: 11/06/2022] [Indexed: 11/10/2022]
Abstract
Aggregation of proteins into amyloid fibrils is driven by interactions between relatively small amyloidogenic segments. The interplay between aggregation-prone and aggregation-resistant fragments within a single polypeptide chain remains obscure. Here, we examine fibrillization behavior of two chimeric peptides, ACC1-13E8 and ACC1-13E8(L/D), in which the highly amyloidogenic fragment of insulin (ACC1-13) is extended by an octaglutamate segment composed of all-L (E8), or alternating L/D residues (E8(L/D)). As separate entities, ACC1-13 readily forms fibrils with the infrared features of parallel β-sheet while E8 forms antiparallel β-sheets with the distinct infrared characteristics. This contrasts with the profoundly aggregation-resistant E8(L/D), although L/D patterns have been hypothesized as compatible with aggregated α-sheets. ACC1-13E8 and ACC1-13E8(L/D) are found to be equally prone to fibrillization at low pH, or in the presence of Ca2+ ions. Fibrillar states of both ACC1-13E8 and ACC1-13E8(L/D) reveal the infrared features of highly ordered parallel β-sheet without evidence of β2-aggregates (ACC1-13E8) or α-sheets (ACC1-13E8(L/D)). Hence, the preferred structural pattern of ACC1-13 overrides the tendency of E8 to form antiparallel β-sheets and enforces the fibrillar order in E8(L/D). We demonstrate how the powerful amyloid stretch determines the overall amyloid structure forcing non-amyloidogenic fragments to participate in its native amyloid pattern.
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Affiliation(s)
- Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur Street 1, 02-093 Warsaw, Poland
| | - Róża Okoń
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur Street 1, 02-093 Warsaw, Poland
| | - Wojciech Puławski
- Bioinformatics Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego Street 5, 02-106 Warsaw, Poland
| | - Matylda Wacławska
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur Street 1, 02-093 Warsaw, Poland
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur Street 1, 02-093 Warsaw, Poland; Institute of High Pressure Physics, Polish Academy of Sciences, Sokołowska Street 29/37, 01-142 Warsaw, Poland.
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Effect of a Short Peptide with Alternating L- and D-Amino Acid on the Aggregation and Membrane Damage of hIAPP. Chem Res Chin Univ 2021. [DOI: 10.1007/s40242-021-0386-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Hayward S, Milner-White EJ. Determination of amino acids that favour the α L region using Ramachandran propensity plots. Implications for α-sheet as the possible amyloid intermediate. J Struct Biol 2021; 213:107738. [PMID: 33838226 DOI: 10.1016/j.jsb.2021.107738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 11/28/2022]
Abstract
In amyloid diseases an insoluble amyloid fibril forms via a soluble oligomeric intermediate. It is this intermediate that mediates toxicity and it has been suggested, somewhat controversially, that it has the α-sheet structure. Nests and α-strands are similar peptide motifs in that alternate residues lie in the αR and γL regions of the Ramachandran plot for nests, or αR and αL regions for α-strands. In nests a concavity is formed by the main chain NH atoms whereas in α-strands the main chain is almost straight. Using "Ramachandran propensity plots" to focus on the αL/γL region, it is shown that glycine favours γL (82% of amino acids are glycine), but disfavours αL (3% are glycine). Most charged and polar amino acids favour αL with asparagine having by far the highest propensity. Thus, glycine favours nests but, contrary to common expectation, should not favour α-sheet. By contrast most charged or polar amino acids should favour α-sheet by their propensity for the αL conformation, which is more discriminating amongst amino acids than the αR conformation. Thus, these results suggest the composition of sequences that favour α-sheet formation and point towards effective prediction of α-sheet from sequence.
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Affiliation(s)
- Steven Hayward
- Computational Biology Laboratory, School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - E James Milner-White
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
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Meng F, Lu T, Wang Y, Zhao Y, Li Z, Li F. Role of Chain Extension in the Ability of Peptide Oligomers to Damage the Lipid Membrane Studied by the l- to d-Amino Acid Substitutions of hIAPP 18-27. J Phys Chem B 2020; 124:10147-10156. [PMID: 33140962 DOI: 10.1021/acs.jpcb.0c07656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exploration of the relation between the structural feature of oligomers and the ability of oligomers to damage the membrane has been an important subject in the study of the cytotoxic mechanism of amyloid proteins. In this work, we selected the hIAPP18-27 fragment as a model peptide and modified it by an alternating substitution of a d-amino acid for an l-amino acid in the hydrophilic N-terminal region, the hydrophobic C-terminal region, and the entire sequence. We prepared the oligomers using these peptides and investigated the effects of chain extension in different regions of the peptide on the ability of the oligomers to damage the membrane composed of POPC/POPG 4:1. We examined the morphology, structure, surface hydrophobicity, and packing compactness of the oligomers and monitored the changes in the structure and aggregation of the peptides upon interaction with the membrane. We found that the surface hydrophobicity and the disruptive ability of the oligomers are increased by an alternating l- and d-amino acid arrangement in the hydrophobic region of the peptide, while the packing compactness of the oligomers is increased and the disruptive ability of the oligomers decreased by an alternating l- and d-amino acid arrangement only in the hydrophilic region. The extension of the hydrophobic chain plays a significant role in the disruptive ability of the oligomers. Our results suggest that a positive relation between the surface hydrophobicity and the disruptive ability could be established only for the oligomers in which the peptide chains are flexible and loosely packed.
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Affiliation(s)
- Feihong Meng
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Avenue, Changchun, 130012, P. R. China
| | - Tong Lu
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Avenue, Changchun, 130012, P. R. China
| | - Yajie Wang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Avenue, Changchun, 130012, P. R. China
| | - Yanping Zhao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, 2699 Qianjin Avenue, Changchun, 130012, P. R. China
| | - Zhengqiang Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, 2699 Qianjin Avenue, Changchun, 130012, P. R. China
| | - Fei Li
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Avenue, Changchun, 130012, P. R. China
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Pignataro MF, Herrera MG, Dodero VI. Evaluation of Peptide/Protein Self-Assembly and Aggregation by Spectroscopic Methods. Molecules 2020; 25:E4854. [PMID: 33096797 PMCID: PMC7587993 DOI: 10.3390/molecules25204854] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023] Open
Abstract
The self-assembly of proteins is an essential process for a variety of cellular functions including cell respiration, mobility and division. On the other hand, protein or peptide misfolding and aggregation is related to the development of Parkinson's disease and Alzheimer's disease, among other aggregopathies. As a consequence, significant research efforts are directed towards the understanding of this process. In this review, we are focused on the use of UV-Visible Absorption Spectroscopy, Fluorescence Spectroscopy and Circular Dichroism to evaluate the self-organization of proteins and peptides in solution. These spectroscopic techniques are commonly available in most chemistry and biochemistry research laboratories, and together they are a powerful approach for initial as well as routine evaluation of protein and peptide self-assembly and aggregation under different environmental stimulus. Furthermore, these spectroscopic techniques are even suitable for studying complex systems like those in the food industry or pharmaceutical formulations, providing an overall idea of the folding, self-assembly, and aggregation processes, which is challenging to obtain with high-resolution methods. Here, we compiled and discussed selected examples, together with our results and those that helped us better to understand the process of protein and peptide aggregation. We put particular emphasis on the basic description of the methods as well as on the experimental considerations needed to obtain meaningful information, to help those who are just getting into this exciting area of research. Moreover, this review is particularly useful to those out of the field who would like to improve reproducibility in their cellular and biomedical experiments, especially while working with peptide and protein systems as an external stimulus. Our final aim is to show the power of these low-resolution techniques to improve our understanding of the self-assembly of peptides and proteins and translate this fundamental knowledge in biomedical research or food applications.
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Affiliation(s)
- María Florencia Pignataro
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
| | - María Georgina Herrera
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Verónica Isabel Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
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