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Qiu J, Tan J. In vitro and in silico analysis of a E559K mutation on cartilage oligomeric matrix protein. Mutat Res 2022; 824:111774. [PMID: 35077910 DOI: 10.1016/j.mrfmmm.2022.111774] [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: 12/02/2019] [Revised: 01/29/2020] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Pseudoachondroplasia (PSACH) is known as an autosomal dominant disorder associated with mutations in the gene of cartilage oligomeric matrix protein (COMP). The pathomolecular mechanisms of PSACH as a result of C-terminal globular region (CTD) mutations remain unclear. A heterozygous mutation (E559 K) in a Chinese family diagnosed with PSACH was reported in this study. To understand the pathogenesis of this mutation, we studied chondrogenic differentiation of patient menstrual blood-derived stem cells (MenSCs), and the impact of the mutation on structural changes of COMP was investigated using all-atom molecular dynamics simulation. The results suggested that the interactions with calcium and other molecules in the mutant structure were affected resulting in misfolding of the protein, which leads to ER stress and finally affects the survival of chondrocytes. The findings may promote the understanding of the pathomolecular mechanisms of PSACH, and possibly the development of drugs to treat the disease.
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Affiliation(s)
- Jiahui Qiu
- Reproductive Medical Center of Gynecology and Obstetrics Department, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, Liaoning, China
| | - Jichun Tan
- Reproductive Medical Center of Gynecology and Obstetrics Department, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, Liaoning, China.
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Tran TT, Pan F, Tran L, Roland C, Sagui C. The F19W mutation reduces the binding affinity of the transmembrane Aβ 11-40 trimer to the membrane bilayer. RSC Adv 2021; 11:2664-2676. [PMID: 35424222 PMCID: PMC8693879 DOI: 10.1039/d0ra08837d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022] Open
Abstract
Alzheimer's disease is linked to the aggregation of the amyloid-β protein (Aβ) of 40 or 42 amino acids. Lipid membranes are known to modulate the rate and mechanisms of the Aβ aggregation. Point mutations in Aβ can alter these rates and mechanisms. In particular, experiments show that F19 mutations influence the aggregation rate, but maintain the fibril structures. Here, we used molecular dynamics simulations to examine the effect of the F19W mutation in the 3Aβ11-40 trimer immersed in DPPC lipid bilayers submerged in aqueous solution. Substituting Phe by its closest (non-polar) aromatic amino acid Trp has a dramatic reduction in binding affinity to the phospholipid membrane (measured with respect to the solvated protein) compared to the wild type: the binding free energy of the protein-DPPC lipid bilayer increases by 40-50 kcal mol-1 over the wild-type. This is accompanied by conformational changes and loss of salt bridges, as well as a more complex free energy surface, all indicative of a more flexible and less stable mutated trimer. These results suggest that the impact of mutations can be assessed, at least partially, by evaluating the interaction of the mutated peptides with the lipid membranes.
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Affiliation(s)
- Thanh Thuy Tran
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Feng Pan
- Department of Statistics, Florida State University Tallahassee Florida USA
| | - Linh Tran
- Institute of Fundamental and Applied Sciences, Duy Tan University Ho Chi Minh City 700000 Vietnam
- Faculty of Natural Sciences, Duy Tan University Da Nang City 550000 Vietnam
| | - Christopher Roland
- Department of Physics, North Carolina State University Raleigh North Carolina USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University Raleigh North Carolina USA
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Saini R, Shuaib S, Goyal D, Goyal B. Impact of Mutations on the Conformational Transition from α-Helix to β-Sheet Structures in Arctic-Type Aβ 40: Insights from Molecular Dynamics Simulations. ACS OMEGA 2020; 5:23219-23228. [PMID: 32954172 PMCID: PMC7495726 DOI: 10.1021/acsomega.0c02983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/13/2020] [Indexed: 05/13/2023]
Abstract
The amyloid-β (Aβ) protein aggregation into toxic oligomers and fibrils has been recognized as a key player in the pathogenesis of Alzheimer's disease. Recent experiments reported that a double alanine mutation (L17A/F19A) in the central hydrophobic core (CHC) region of [G22]Aβ40 (familial Arctic mutation) diminished the self-assembly propensity of [G22]Aβ40. However, the molecular mechanism behind the decreased aggregation tendency of [A17/A19/G22]Aβ40 is not well understood. Herein, we carried out molecular dynamics simulations to elucidate the structure and dynamics of [G22]Aβ40 and [A17/A19/G22]Aβ40. The results for the secondary structure analysis reveal a significantly increased amount of the helical content in the CHC and C-terminal region of [A17/A19/G22]Aβ40 as compared to [G22]Aβ40. The bending free-energy analysis of D23-K28 salt bridge suggests that the double alanine mutation in the CHC region of [G22]Aβ40 has the potential to reduce the fibril formation rate by 0.57 times of [G22]Aβ40. Unlike [G22]Aβ40, [A17/A19/G22]Aβ40 largely sampled helical conformation, as determined by the minimum energy conformations extracted from the free-energy landscape. The present study provided atomic level details into the experimentally observed diminished aggregation tendency of [A17/A19/G22]Aβ40 as compared to [G22]Aβ40.
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Affiliation(s)
- Rajneet
Kaur Saini
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Suniba Shuaib
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Deepti Goyal
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Bhupesh Goyal
- School
of Chemistry & Biochemistry, Thapar
Institute of Engineering & Technology, Patiala 147004, Punjab, India
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Saini RK, Thakur H, Goyal B. Effect of Piedmont mutation (L34V) on the structure, dynamics, and aggregation of Alzheimer's Aβ 40 peptide. J Mol Graph Model 2020; 97:107571. [PMID: 32143150 DOI: 10.1016/j.jmgm.2020.107571] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/26/2020] [Accepted: 02/19/2020] [Indexed: 12/22/2022]
Abstract
The amyloid-β (Aβ) aggregation in the brain has been associated with the development of Alzheimer's disease (AD). The previous studies have reported that Piedmont mutation (L34V) increases the rate of Aβ40 aggregation. However, the underlying molecular mechanism of the effect of L34V mutation on Aβ40 structure, dynamics, and aggregation remains largely unclear. In the present study, molecular dynamics (MD) simulations were performed to elucidate the effect of L34V mutation on the structural changes and conformational dynamics of Aβ40. The secondary structure analysis highlight that L34V mutation enhances Aβ40 self-assembly due to the formation of aggregation-prone β-sheet structure at the C-terminus of Aβ40 monomeric structure. The higher probability of Asp23-Lys28 salt bridge interaction in Aβ40(L34V) leads to aggregation prone β-sheet conformations, which has the potential to increase the fibril formation rate. The free energy landscape (FEL) analysis depict a sampling of coil conformation in the free energy minima of Aβ40, whereas the aggregation-prone β-sheet conformation was observed at the C-terminal region of Aβ40(L34V) in the minimum energy conformations extracted from FEL of Aβ40(L34V). MD simulations, in agreement with experiment, highlight that L34V mutation increases Aβ40 aggregation as the sampling of the aggregation-prone β-sheet conformation substantially increased. Overall, MD simulations provided atomic level details into the increased fibril formation tendency upon L34V mutation and physical insights into the L34V-mediated conformational as well as structural changes in Aβ40.
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Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, 140406, Punjab, India
| | - Hema Thakur
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India.
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Liu WS, Wang RR, Sun YZ, Li WY, Li HL, Liu CL, Ma Y, Wang RL. Exploring the effect of inhibitor AKB-9778 on VE-PTP by molecular docking and molecular dynamics simulation. J Cell Biochem 2019; 120:17015-17029. [PMID: 31125141 DOI: 10.1002/jcb.28963] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/03/2019] [Accepted: 03/15/2019] [Indexed: 01/02/2023]
Abstract
Diabetic macular edema, also known as diabetic eye disease, is mainly caused by the overexpression of vascular endothelial protein tyrosine phosphatase (VE-PTP) at hypoxia/ischemic. AKB-9778 is a known VE-PTP inhibitor that can effectively interact with the active site of VE-PTP to inhibit the activity of VE-PTP. However, the binding pattern of VE-PTP with AKB-9778 and the dynamic implications of AKB-9778 on VE-PTP system at the molecular level are poorly understood. Through molecular docking, it was found that the AKB-9778 was docked well in the binding pocket of VE-PTP by the interactions of hydrogen bond and Van der Waals. Furthermore, after molecular dynamic simulations on VE-PTP system and VE-PTP AKB-9778 system, a series of postdynamic analyses found that the flexibility and conformation of the active site undergone an obvious transition after VE-PTP binding with AKB-9778. Moreover, by constructing the RIN, it was found that the different interactions in the active site were the detailed reasons for the conformational differences between these two systems. Thus, the finding here might provide a deeper understanding of AKB-9778 as VE-PTP Inhibitor.
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Affiliation(s)
- Wen-Shan Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying-Zhan Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hong-Lian Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Chi-Lu Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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Wang RR, Ma Y, Du S, Li WY, Sun YZ, Zhou H, Wang RL. Exploring the reason for increased activity of SHP2 caused by D61Y mutation through molecular dynamics. Comput Biol Chem 2019; 78:133-143. [DOI: 10.1016/j.compbiolchem.2018.10.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/26/2018] [Accepted: 10/26/2018] [Indexed: 01/01/2023]
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