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Sun Y, Shi Y, Li C, Shi H. Histidine Protonation Behaviors on Structural Properties and Aggregation Properties of Aβ(1-42) Mature Fibril: Approaching by Edge Effects. J Phys Chem B 2024. [PMID: 39018428 DOI: 10.1021/acs.jpcb.4c02343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
The histidine behavior plays a crucial role in the structural and aggregation properties of protein folding and misfolding. Understanding the histidine behavior at the edge of the protein structure is critical for finding ways to disrupt fibril elongation and growth, but this impact remains poorly understood. In the current study, we used molecular dynamics simulations to investigate the edge substitution effect of histidine protonation on the structural and aggregation properties. Our data showed that ΔG1 contributed the most to binding affinity compared to ΔG2 and ΔG3. The different protonation states at the edge chain significantly impacted the secondary structure properties of the edge chain. Specifically, we found that such protonation behavior significantly affected specific regions, particularly the N-terminus (G9-Q15) and C-terminus (K28-A30). Further analysis confirmed that H6, H13, and H14 were directly involved in H-bonding networks with the C1_H14//C2_H13 interchain interactions critical for maintaining the interchain stability. Furthermore, we confirmed that H6, H13, and H14 were directly involved in the loss of the carbon skeleton contact in the N-terminus. Our findings indicate that the edge condition is more susceptible to changes in structural properties than the middle condition. The current study is helpful for understanding the histidine behavior hypothesis in related misfolding diseases.
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Affiliation(s)
- Yue Sun
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Yaru Shi
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Changgui Li
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Hu Shi
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
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Song Y, Wu M, Wang C, Fang H, Lei X. Zn 2+ Binding Increases Parallel Structure in the Aβ(16-22) Oligomer by Disrupting Salt Bridge in Antiparallel Structure. J Phys Chem B 2024; 128:1385-1393. [PMID: 38294417 DOI: 10.1021/acs.jpcb.3c06925] [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: 02/01/2024]
Abstract
The aggregation of monomeric amyloid β protein (Aβ) into oligomers and amyloid plaque in the brain is associated with Alzheimer's disease. The hydrophobic central core Aβ16-22 has been widely studied due to its essential role in the fibrillization of full-length Aβ peptides. Compared to the homogeneous antiparallel structure of Aβ16-22 at the late stage, the early-stage prefibrillar aggregates contain varying proportions of different β structures. In this work, we studied the appearance probabilities of various self-assembly structures of Aβ16-22 and the effects of Zn2+ on these probabilities by replica exchange molecular dynamics simulations. It was found that at room temperature, Aβ16-22 can readily form assembled β-sheet structures in pure water, where a typical antiparallel arrangement dominates (24.8% of all sampled trimer structures). The addition of Zn2+ to the Aβ16-22 solution will dramatically decrease the appearance probability of antiparallel trimer structures to 12.5% by disrupting the formation of the Lys16-Glu22 salt bridge. Meanwhile, the probabilities of hybrid antiparallel/parallel structures increase. Our simulation results not only reveal the competition between antiparallel and parallel structures in the Aβ16-22 oligomers but also show that Zn2+ can affect the oligomer structures. The results also provide insights into the role of metal ions in the self-assembly of short peptides.
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Affiliation(s)
- Yongshun Song
- School of Physics, East China University of Science and Technology, Shanghai 200237, China
| | - Mengjiao Wu
- School of Physics, East China University of Science and Technology, Shanghai 200237, China
| | - Changying Wang
- School of Sciences, Changzhou Institute of Technology, Changzhou 213032, China
| | - Haiping Fang
- School of Physics, East China University of Science and Technology, Shanghai 200237, China
- Department of Physics, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoling Lei
- School of Physics, East China University of Science and Technology, Shanghai 200237, China
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Yan L, Deng Y, Du Y, Fang X, Fang X, Zhang Q. Metabolic Regulations of Smilax china L. against β-Amyloid Toxicity in Caenorhabditis elegans. Metabolites 2024; 14:49. [PMID: 38248852 PMCID: PMC10818737 DOI: 10.3390/metabo14010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
Smilax china L. (Chinaroot) is a natural herb that has multiple uses, such as being used to make tea and food. Both its roots and leaves have different uses due to their unique components. In this study, we analyzed the extract of S. china. roots using LC-HRMS and evaluated the neuroprotective effects and metabolic regulation of S. china on Caenorhabditis elegans. Chinaroot extract prolonged the life span of healthy nematodes, delayed the paralysis time of transgenic CL4176, and reduced the level of β-amyloid deposition in transgenic CL2006. The comprehensive analysis of metabolomics and qRT-PCR revealed that Chinaroot extract exerted neuroprotective effects through the valine, leucine and isoleucine degradation and fatty acid degradation pathways. Moreover, we first discovered that the expressions of T09B4.8, ech-7, and agxt-1 were linked to the neuroprotective effects of Chinaroot. The material exerted neuroprotective effects by modulating metabolic abnormalities in AD model C. elegans. Our study provides a new foundation for the development of functional food properties and functions.
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Affiliation(s)
- Lili Yan
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Yuchan Deng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Yulan Du
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Xutong Fang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Xin Fang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Qiang Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
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Sun Y, Yao Z, Wang G, Wang L, Bai M, Shi H. Concentration Effect, Structural Properties, and Driving Force on Aβ 28 Dimerization with and without Zn 2+ Cooperation: Learning from Replica Exchange Sampling. Chemphyschem 2023; 24:e202200710. [PMID: 36427251 DOI: 10.1002/cphc.202200710] [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: 09/21/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 11/26/2022]
Abstract
Zn2+ is a very important factor in promoting the formation of amyloid beta (Aβ) aggregates and amyloid plaques. The Zn2+ -bound Aβ species generate amorphous or low molecular-weight oligomers. However, it is a lack of studies to approach the starting structural features (dimerization) in Aβ nucleation processes with and without Zn2+ , which is the key point in understanding Zn2+ -induced nucleation mechanisms. To better understand the effect of concentration, structural properties, and the driving force, 14 independent replica exchange molecular dynamics simulations were performed in Aβ28 dimerization with and without Zn2+ (zAβ28 ) cooperation. Our scanning results show that the aggregation propensity is easier in Aβ28 -Aβ28 and Aβ28 -zAβ28 systems than zAβ28 -zAβ28 system. In binding property, the Aβ28 -Aβ28 model (-61.5 kcal mol-1 ) is stronger than zAβ28 -zAβ28 (-26.6 kcal mol-1 ) and Aβ28 -zAβ28 (-7.24 kcal mol-1 ) models. Further analysis confirmed that H13 and H14 residues play specific roles in the three systems. The key point is the orientation of N atom of the imidazole ring in histidine residues. Furthermore, we discovered different driving forces for each system. Our current study contributes to the understanding of how the Aβ28 dimer interacts with Zn2+ , which could lead to new insights into Zn2+ -induced nucleation mechanisms.
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Affiliation(s)
- Yue Sun
- School of Chemistry and Chemical Engineering, Shanxi University, 030006, Taiyuan, China
| | - Zeshuai Yao
- School of Chemistry and Chemical Engineering, Shanxi University, 030006, Taiyuan, China
| | - Guangyu Wang
- School of Chemistry and Chemical Engineering, Shanxi University, 030006, Taiyuan, China
| | - Lisha Wang
- School of Chemistry and Chemical Engineering, Shanxi University, 030006, Taiyuan, China
| | - Min Bai
- Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, 030006, Taiyuan, China
| | - Hu Shi
- School of Chemistry and Chemical Engineering, Shanxi University, 030006, Taiyuan, China.,Institute of Molecular Science, Shanxi University, 030006, Taiyuan, China
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Islam M, Argueta E, Wojcikiewicz EP, Du D. Effects of Charged Polyelectrolytes on Amyloid Fibril Formation of a Tau Fragment. ACS Chem Neurosci 2022; 13:3034-3043. [PMID: 36219395 PMCID: PMC10249396 DOI: 10.1021/acschemneuro.2c00374] [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] [Indexed: 01/20/2023] Open
Abstract
The microtubule-associated protein tau is involved in more than 20 different neurological disorders characterized by aberrant intracellular aggregation of tau in the brain. Here, we investigated the aggregation of a novel 20-residue model peptide, tau298-317, which is derived from the key microtubule binding domain of the full sequence tau. Our results show that tau298-317 highly mimics the physical and aggregation properties of tau. Under normal physiological conditions, the peptide maintains a disordered random coil without aggregation. The presence of polyanionic heparin (Hep) significantly promotes the aggregation of this peptide to form amyloid fibrils. The Hep-induced aggregation is sensitive to the ionic strength of the solution and the introduction of the negatively charged phosphate group on a serine (Ser305) residue in the sequence, suggesting an important role of electrostatic interactions in the mechanism of Hep-mediated aggregation. In addition, two positively charged polysaccharides, chitosan (CHT) and its quaternary derivative N-trimethyl chitosan (TMC), were found to effectively inhibit Hep-induced aggregation of tau298-317 in a concentration-dependent manner. Attractive electrostatic interactions between the positively charged moieties in CHT/TMC and the negatively charged residues of Hep play a critical role in inhibiting Hep-peptide interactions and suppressing peptide aggregation. Our results suggest that positively charged polyelectrolytes with optimized charged groups and charge distribution patterns can serve as effective molecular candidates to block tau-Hep interactions and prevent aggregation of tau induced by Hep and other polyanions.
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Affiliation(s)
- Majedul Islam
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Emily Argueta
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Ewa P. Wojcikiewicz
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Deguo Du
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
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