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Sahoo BR, Ramamoorthy A. Direct interaction between the transmembrane helices stabilize cytochrome P450 2B4 and cytochrome b5 redox complex. Biophys Chem 2023; 301:107092. [PMID: 37586236 PMCID: PMC10838600 DOI: 10.1016/j.bpc.2023.107092] [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] [Received: 06/12/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/18/2023]
Abstract
The catalytic activity of cytochrome P450 2B4 (CYP2B4) is moderated by its cognate redox partner cytochrome b5 (Cyt-b5). The endoplasmic reticulum (ER) membrane and intermolecular transmembrane (TM) interaction between CYP2B4 and Cyt-b5 regulate the substrate catalysis and the reaction rate. This emphasizes the significance of elucidating the molecular basis of CYP2B4 and Cyt-b5 complexation in a membrane environment to better understand the enzymatic activity of CYP2B4. Our previous solid-state NMR studies revealed the membrane topology of the transmembrane domains of these proteins in the free and complex forms. Here, we show the cross-angle complex formation by the single-pass TM domains of CYP2B4 and Cyt-b5, which is mainly driven by several salt-bridges (E2-R128, R21-D104 and K25-D104), using a multi-microsecond molecular dynamic simulation. Additionally, the leucine-zipper residues (L8, L12, L15, L18 and L19 from CYP2B4) and π-stacking between H23 and F20 residues of CYP2B4 and W110 of Cyt-b5 are identified to stabilize the TM-TM complex in the ER membrane. The simulated tilts of the helices in the free and in the complex are in excellent agreement with solid-state NMR results. The TM-TM packing influences a higher order structural stability when compared to the complex formed by the truncated soluble domains of these two proteins. MM/PBSA based binding free energy estimates nearly 100-fold higher binding affinity (ΔG = -2810.68 ± 696.44 kJ/mol) between the soluble domains of the full-length CYP2B4 and Cyt-b5 when embedded in lipid membrane as compared to the TM-domain-truncated soluble domains (ΔG = -27.406 ± 10.32 kJ/mol). The high-resolution full-length CYP2B4-Cyt-b5 complex structure and its dynamics in a native ER membrane environment reported here could aid in the development of approaches to effectively modulate the drug-metabolism activity of CYP2B4.
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Affiliation(s)
- Bikash R Sahoo
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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2
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Interaction, bioaccessibility and stability of bovine serum albumin-gamma-oryzanol complex: Spectroscopic and computational approaches. Food Chem 2023; 402:134493. [DOI: 10.1016/j.foodchem.2022.134493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 08/15/2022] [Accepted: 09/29/2022] [Indexed: 01/30/2023]
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Xiao J, Wang J, Gan R, Wu D, Xu Y, Peng L, Geng F. Quantitative N-glycoproteome analysis of bovine milk and yogurt. Curr Res Food Sci 2022; 5:182-190. [PMID: 35072106 PMCID: PMC8763629 DOI: 10.1016/j.crfs.2022.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/25/2021] [Accepted: 01/05/2022] [Indexed: 12/02/2022] Open
Abstract
Post-translational modification structure of food's proteins might be changed during processing, thereby affecting the nutritional characteristics of the food product. In this study, differences in protein N-glycosylation patterns between milk and yogurt were quantitatively compared based on glycopeptide enrichment, liquid chromatography separation, and tandem mass spectrometry analysis. A total of 181 N-glycosites were identified, among which 142 were quantified in milk and yogurt. Significant alterations in the abundance of 13 of these N-glycosites were evident after the fermentation of milk into yogurt. Overall, the N-glycosylation status of the majority of milk proteins remained relatively unchanged in yogurt, suggesting that their conformations, activities, and functions were maintained despite the fermentation process. Among the main milk proteins, N241 of cathepsin D and N358 of lactoperoxidase were markedly reduced after undergoing lactic acid fermentation to produce yogurt. Furthermore, a comparative analysis of current and previously reported N-glycoproteomic data revealed heterogeneity in the N-glycosylation of milk proteins. To sum up, a quantitative comparison of the N-glycoproteomes of milk and yogurt was presented here for the first time, providing evidence that the fermentation process of yogurt could cause changes in the N-glycosylation of certain milk proteins. 181 N-glycosites from 118 N-glycoproteins were identified in milk and yogurt. 13 N-glycosites changed significantly after fermentation of milk into yogurt. N241 of cathepsin D and N358 of lactoperoxidase was markedly reduced in yogurt. Heterogeneity of N-glycosylation of milk protein has been documented.
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Affiliation(s)
- Jing Xiao
- Key Laboratory of Coarse Cereal Processing (Ministry of Agriculture and Rural Affairs), School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Jinqiu Wang
- Key Laboratory of Coarse Cereal Processing (Ministry of Agriculture and Rural Affairs), School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Renyou Gan
- Research Center for Plants and Human Health, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610213, Sichuan, China
| | - Di Wu
- Key Laboratory of Coarse Cereal Processing (Ministry of Agriculture and Rural Affairs), School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Yisha Xu
- Key Laboratory of Coarse Cereal Processing (Ministry of Agriculture and Rural Affairs), School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing (Ministry of Agriculture and Rural Affairs), School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Fang Geng
- Key Laboratory of Coarse Cereal Processing (Ministry of Agriculture and Rural Affairs), School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China
- Corresponding author.
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Chen Z, Yang X, Bi G, Liang J, Hu Z, Zhao M, Li M, Lu T, Zheng Y, Sui Q, Yang Y, Zhan C, Jiang W, Wang Q, Tan L. Ligand-receptor interaction atlas within and between tumor cells and T cells in lung adenocarcinoma. Int J Biol Sci 2020; 16:2205-2219. [PMID: 32549766 PMCID: PMC7294944 DOI: 10.7150/ijbs.42080] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/02/2020] [Indexed: 12/31/2022] Open
Abstract
Purpose: Lung adenocarcinoma (LUAD) is the leading cause of cancer-related deaths worldwide. Although tumor cell-T cell interactions are known to play a fundamental role in promoting tumor progression, these interactions have not been explored in LUAD. Methods: The 10x genomics single-cell RNA sequencing (scRNA-seq) and gene expression data of LUAD patients were obtained from ArrayExpress, TCGA, and GEO databases. scRNA-seq data were analyzed and infiltrating tumor cells, epithelial cells, and T cells were identified in the tumor microenvironment. Differentially expressed ligand-receptor pairs were identified in tumor cells/normal epithelial cells and tumor T cells/non-tumor T cells based on corresponding scRNA-seq and gene expression data, respectively. These important interactions inside/across cancer cells and T cells in LUAD were systematically analyzed. Furthermore, a valid prognostic machine-learning model based on ligand-receptor interactions was built to predict the prognosis of LUAD patients. Flow cytometry and qRT-PCR were performed to validate the significantly differently expressed ligand-receptor pairs. Results: Overall, 39,692 cells in scRNA-seq data were included in our study after quality filtering. A total of 65 ligand-receptor pairs (17 upregulated and 48 downregulated), including LAMB1-ITGB1, CD70-CD27, and HLA-B-LILRB2, and 96 ligand-receptor pairs (41 upregulated and 55 downregulated), including CCL5-CCR5, SELPLG-ITGB2, and CXCL13-CXCR5, were identified in LUAD cancer cells and T cells, respectively. To explore the crosstalk between cancer cells and T cells, 114 ligand-receptor pairs, including 11 ligand-receptor pair genes that could significantly affect survival outcomes, were identified in our research. A machine-learning model was established to accurately predict the prognosis of LUAD patients and ITGB4, CXCR5, and MET were found to play an important role in prognosis in our model. Flow cytometry and qRT-PCR analyses indicated the reliability of our study. Conclusion: Our study revealed functionally significant interactions within and between cancer cells and T cells. We believe these observations will improve our understanding of potential mechanisms of tumor microenvironment contributions to cancer progression and help identify potential targets for immunotherapy in the future.
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Affiliation(s)
- Zhencong Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Xiaodong Yang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Guoshu Bi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Zhengyang Hu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Mengnan Zhao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Ming Li
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Tao Lu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Yuansheng Zheng
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Qihai Sui
- Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yong Yang
- Department of Thoracic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215001, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Wei Jiang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Lijie Tan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
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Ghosh M, Gayen S, Dey KK. An atomic resolution description of folic acid using solid state NMR measurements. RSC Adv 2020; 10:24973-24984. [PMID: 35517491 PMCID: PMC9055165 DOI: 10.1039/d0ra03772a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/15/2020] [Indexed: 11/21/2022] Open
Abstract
The chemical shift anisotropy tensor and site-specific spin-lattice relaxation time of folic acid were determined by a 13C 2DPASS CP-MAS NMR experiment and Torchia CP experiment respectively. The molecular correlation time at various carbon nuclei sites of folic acid was evaluated by assuming that the 13C spin-lattice relaxation mechanism is mainly governed by chemical shift anisotropy interaction and hetero-nuclear dipole–dipole coupling. CSA parameters are larger for the carbon nuclei residing at the heteroaromatic ring and aromatic ring, and those attached to double-bonded electronegative oxygen atoms. It is comparatively low for C9, C19, C21, and C22. The molecular correlation time is of the order of 10−4/10−5 s for C9, C19, C21 and C22 carbon nuclei, whereas it is of the order of 10−3 s for the rest of the carbon nuclei sites. Spin lattice relaxation time varies from 416 s to 816 s. For C23 and C14, the value is 816 s, and it is 416 s for C7 nuclei. The correlation between structure and dynamics on an atomic scale of such an important drug as folic acid can be visualized by these types of extensive spectroscopic measurements, which will help to develop an advanced drug for DNA replication. The chemical shift anisotropy tensor and site specific spin-lattice relaxation time of folic acid were determined by a 13C 2DPASS CP-MAS NMR experiment and Torchia CP experiment respectively.![]()
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Affiliation(s)
- Manasi Ghosh
- Department of Physics
- Dr Harisingh Gour Central University
- Sagar-470003
- India
| | - Shovanlal Gayen
- Department of Pharmaceutical Sciences
- Dr Harisingh Gour Central University
- Sagar-470003
- India
| | - Krishna Kishor Dey
- Department of Physics
- Dr Harisingh Gour Central University
- Sagar-470003
- India
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Sahoo BR, Bekier ME, Liu Z, Kocman V, Stoddard AK, Anantharamaiah GM, Nowick J, Fierke CA, Wang Y, Ramamoorthy A. Structural Interaction of Apolipoprotein A-I Mimetic Peptide with Amyloid-β Generates Toxic Hetero-oligomers. J Mol Biol 2019; 432:1020-1034. [PMID: 31866295 DOI: 10.1016/j.jmb.2019.12.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 01/21/2023]
Abstract
Apolipoproteins are involved in pathological conditions of Alzheimer's disease (AD), and it has been reported that truncated apolipoprotein fragments and β-amyloid (Aβ) peptides coexist as neurotoxic heteromers within the plaques. Therefore, it is important to investigate these complexes at the molecular level to better understand their properties and roles in the pathology of AD. Here, we present a mechanistic insight into such heteromerization using a structurally homologue apolipoprotein fragment of apoA-I (4F) complexed with Aβ(M1-42) and characterize their toxicity. The 4F peptide slows down the aggregation kinetics of Aβ(M1-42) by constraining its structural plasticity. NMR and CD experiments identified 4F-Aβ(M1-42) heteromers comprised of unstructured Aβ(M1-42) and helical 4F. A uniform two-fold reduction in 15N/1H NMR signal intensities of Aβ(M1-42) with no observable chemical shift perturbation indicated the formation of a large complex, which was further confirmed by diffusion NMR experiments. Microsecond-scale atomistic molecular dynamics simulations showed that 4F interaction with Aβ(M1-42) is electrostatically driven and induces unfolding of Aβ(M1-42). Neurotoxicity profiling of Aβ(M1-42) complexed with 4F confirms a significant reduction in cell viability and neurite growth. Thus, the molecular architecture of heteromerization between 4F and Aβ(M1-42) discovered in this study provides evidence toward our understanding of the role of apolipoproteins or their truncated fragments in exacerbating AD pathology.
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Affiliation(s)
- Bikash Ranjan Sahoo
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Michael E Bekier
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA
| | - Zichen Liu
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Vojc Kocman
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Andrea K Stoddard
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - G M Anantharamaiah
- Department of Medicine, University of Alabama at Birmingham Medical Center, Birmingham, AL, 35294, USA
| | - James Nowick
- Department of Chemistry, University of California-Irvine, Irvine, CA, 92697-2025, USA
| | - Carol A Fierke
- Department of Chemistry, University of Texas A&M, College Station, TX, 77843-3255, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA.
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Sahoo BR, Genjo T, Moharana KC, Ramamoorthy A. Self-Assembly of Polymer-Encased Lipid Nanodiscs and Membrane Protein Reconstitution. J Phys Chem B 2019; 123:4562-4570. [DOI: 10.1021/acs.jpcb.9b03681] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Kanhu C. Moharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, Odisha 751003, India
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8
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Sahoo BR, Genjo T, Nakayama TW, Stoddard AK, Ando T, Yasuhara K, Fierke CA, Ramamoorthy A. A cationic polymethacrylate-copolymer acts as an agonist for β-amyloid and an antagonist for amylin fibrillation. Chem Sci 2019; 10:3976-3986. [PMID: 31015938 PMCID: PMC6457205 DOI: 10.1039/c8sc05771k] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/25/2019] [Indexed: 12/24/2022] Open
Abstract
In humans, β-amyloid and islet amyloid polypeptide (IAPP, also known as amylin) aggregations are linked to Alzheimer's disease and type-2 diabetes, respectively. There is significant interest in better understanding the aggregation process by using chemical tools. Here, we show the ability of a cationic polymethacrylate-copolymer (PMAQA) to quickly induce a β-hairpin structure and accelerate the formation of amorphous aggregates of β-amyloid-1-40, whereas it constrains the conformational plasticity of amylin for several days and slows down its aggregation at substoichiometric polymer concentrations. NMR experiments and microsecond scale atomistic molecular dynamics simulations reveal that PMAQA interacts with β-amyloid-1-40 residues spanning regions K16-V24 and A30-V40 followed by β-sheet induction. For amylin, it binds strongly close to the amyloid core domain (NFGAIL) and restrains its structural rearrangement. High-speed atomic force microscopy and transmission electron microscopy experiments show that PMAQA blocks the nucleation and fibrillation of amylin, whereas it induces the formation of amorphous aggregates of β-amyloid-1-40. Thus, the reported study provides a valuable approach to develop polymer-based amyloid inhibitors to suppress the formation of toxic intermediates of β-amyloid-1-40 and amylin.
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Affiliation(s)
- Bikash R Sahoo
- Biophysics and Department of Chemistry , University of Michigan , Ann Arbor , MI 48109-1055 , USA .
| | - Takuya Genjo
- Biophysics and Department of Chemistry , University of Michigan , Ann Arbor , MI 48109-1055 , USA .
| | - Takahiro W Nakayama
- Bio-AFM Frontier Research Center , Kanazawa University , Kanazawa 920-1192 , Japan
| | - Andrea K Stoddard
- Biophysics and Department of Chemistry , University of Michigan , Ann Arbor , MI 48109-1055 , USA .
| | - Toshio Ando
- Bio-AFM Frontier Research Center , Kanazawa University , Kanazawa 920-1192 , Japan
| | - Kazuma Yasuhara
- Graduate School of Materials Science , Nara Institute of Science and Technology , Ikoma , Nara 6300192 , Japan
| | - Carol A Fierke
- Biophysics and Department of Chemistry , University of Michigan , Ann Arbor , MI 48109-1055 , USA .
- Department of Chemistry , Texas A&M University , College Station , TX 77843 , USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry , University of Michigan , Ann Arbor , MI 48109-1055 , USA .
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9
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Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 332] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
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10
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Wang C, Jiang Y, Fei X, Gu Y. Design and interaction mechanism of ligand targeted with folate receptor α and β. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- C. Wang
- School of Science; TianJin ChengJian University; Tianjin China
| | - Y. Jiang
- School of Science; TianJin ChengJian University; Tianjin China
| | - X. Fei
- School of Science; TianJin ChengJian University; Tianjin China
| | - Y. Gu
- School of Science; TianJin ChengJian University; Tianjin China
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11
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Sahoo BR, Fujiwara T. Conformational states of HAMP domains interacting with sensory rhodopsin membrane systems: an integrated all-atom and coarse-grained molecular dynamics simulation approach. MOLECULAR BIOSYSTEMS 2017; 13:193-207. [PMID: 27901172 DOI: 10.1039/c6mb00730a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Understanding the downstream signaling mechanism of sensory rhodopsin and its cognate transducer complex (srII-htrII) has long been a challenge in the field of photoreceptor research. Here, an integration of all-atom and coarse-grained (CG) molecular dynamics (MD) simulations in different srII-htrII complex states is carried out. It is shown that the cytoplasmic four-helix HAMP dimer gives rise to a gear-box model interaction with discrete hydrophobic packing in Natronomonas pharaonis (Np). Structural analysis in all-atom and CG-MD reveals a stable conformational state in the physiological environment (323 K and 1.15 M salt). Comparative analysis in the ground and intermediate state conformations reveals substantial inter-HAMP interactions in the intermediate state with uniform clockwise (+10° to +30°) and counterclockwise (-20° to -40°) rotations in the α1 helix and the α2 helix of the monomer, respectively. Low temperature and low salt environments (283 K and 0.15 M) significantly affect srII-htrII binding affinity in both states with unusual helix bending. The distinguished control cable, knob-into-holes packing and piston-like movements in HAMP helices are found in the intermediate state complex. The N-terminal htrII (159 residues) coupled with srII yields a binding energy (ΔGbind) of -309.22, -436.53 and -331.11 kJ mol-1 in the MM/PBSA calculation for the NphtrII homodimer, the NpsrII-htrII ground state conformation and the NpsrII-htrII intermediate state conformation, respectively. Only the HAMP1 domain shows a very low ΔGbind value (-21.03 kJ mol-1) for the ground state in comparison to that for the intermediate state (-54.68 kJ mol-1). The structural analysis highlights the key residues that include Y199srII, T189srII, E43htrII, T86htrII, M100htrII, E116htrII, E126htrII and S130htrII for complex stabilization and signal transduction.
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Affiliation(s)
- Bikash Ranjan Sahoo
- Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, 5650871, Japan.
| | - Toshimichi Fujiwara
- Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, 5650871, Japan.
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12
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Synthesis and biological assessment of folate-accepted developer (99m)Tc-DTPA-folate-polymer. Bioorg Med Chem Lett 2016; 26:2547-2550. [PMID: 27072904 DOI: 10.1016/j.bmcl.2016.03.084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 03/09/2016] [Accepted: 03/25/2016] [Indexed: 11/21/2022]
Abstract
A novel cancer-targetable folate-poly(2-hydroxyethyl methacrylate) (PFDH) copolymer containing DTPA segment was prepared by conventional chemical synthesis and labeled with (99m)Tc subsequently. The (99m)Tc-labled PFDH could be produced easily with high radiochemical yield of 91% and radiochemical purity of 95%. The LogP octanol-water value for the (99m)Tc-labled PFDH was -2.19 and the radiotracer was stable in phosphate-buffered saline and human serum for 2h (>95% in PBS or ∼90% in human serum). To investigate (99m)Tc-labled PFDH tumor targeting, the in vitro and in vivo stability, cell uptake, in vivo biodistribution, and SPECT imaging were evaluated, respectively. These preliminary results strongly suggest that the novel folate conjugated dendrimer maybe developed to be potential for delivery of therapeutic radionuclides.
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Leroueil PR, DiMaggio S, Leistra AN, Blanchette CD, Orme C, Sinniah K, Orr BG, Banaszak Holl MM. Characterization of Folic Acid and Poly(amidoamine) Dendrimer Interactions with Folate Binding Protein: A Force-Pulling Study. J Phys Chem B 2015; 119:11506-12. [PMID: 26256755 DOI: 10.1021/acs.jpcb.5b05391] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atomic force microscopy force-pulling experiments have been used to measure the binding forces between folic acid (FA) conjugated poly(amidoamine) (PAMAM) dendrimers and folate binding protein (FBP). The generation 5 (G5) PAMAM conjugates contained an average of 2.7, 4.7, and 7.2 FA per dendrimer. The most probable rupture force was measured to be 83, 201, and 189 pN for G5-FA2.7, G5-FA4.7, and G5-FA7.2, respectively. Folic acid blocking experiments for G5-FA7.2 reduced the frequency of successful binding events and increased the magnitude of the average rupture force to 274 pN. The force data are interpreted as arising from a network of van der Waals and electrostatic interactions that form between FBP and G5 PAMAM dendrimer, resulting in a binding strength far greater than that expected for an interaction between FA and FBP alone.
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Affiliation(s)
| | - Stassi DiMaggio
- Department of Chemistry, Xavier University , New Orleans, Louisiana 70125, United States
| | - Abigail N Leistra
- Department of Chemistry & Biochemistry, Calvin College , Grand Rapids, Michigan 49546, United States
| | - Craig D Blanchette
- Physical and Life Sciences Division, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
| | - Christine Orme
- Physical and Life Sciences Division, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
| | - Kumar Sinniah
- Department of Chemistry & Biochemistry, Calvin College , Grand Rapids, Michigan 49546, United States
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14
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Holm J, Bruun SW, Hansen SI. The complex interplay between ligand binding and conformational structure of the folate binding protein (folate receptor): Biological perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1249-59. [PMID: 26116148 DOI: 10.1016/j.bbapap.2015.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/05/2015] [Accepted: 06/23/2015] [Indexed: 11/27/2022]
Abstract
This review analyzes how interplay between folate binding and changes in folate binding protein (FBP) conformation/self-association affects the biological function of FBP. Concentration-dependent, reversible self-association of hydrophobic apo-FBP at pI=7.4 is associated with decreased affinity for folate, probably due to shielding of binding sites between interacting hydrophobic patches. Titration with folate removes apo-monomers, favoring dissociation of self-associated apo-FBP into apo-monomers. Folate anchors to FBP through a network of hydrogen bonds and hydrophobic interactions, and the binding induces a conformational change with formation of hydrophilic and stable holo-FBP. Holo-FBP exhibits a ligand-mediated concentration-dependent self-association into multimers of great thermal and chemical stability due to strong intermolecular forces. Both ligand and FBP are thus protected against biological/physicochemical decomposition. In biological fluids with low FBP concentrations, e.g., saliva, semen and plasma, hydrophobic apo-monomers and hydrophilic holo-monomers associate into stable asymmetrical complexes with aberrant binding kinetics unless detergents, e.g., cholesterol or phospholipids are present.
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Affiliation(s)
- Jan Holm
- Department of Clinical Biochemistry, Nordsjællands Hospital - Hillerød, University Hospital Copenhagen, Dyrehavevej 29, DK-3400 Hillerød, Denmark.
| | - Susanne W Bruun
- Faculty of Science, Department of Food Science, Spectroscopy and Chemometrics, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg, Denmark
| | - Steen I Hansen
- Department of Clinical Biochemistry, Nordsjællands Hospital - Hillerød, University Hospital Copenhagen, Dyrehavevej 29, DK-3400 Hillerød, Denmark.
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15
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Sahoo BR, Dubey PK, Goyal S, Bhoi GK, Lenka SK, Maharana J, Pradhan SK, Kataria RS. Exploration of the binding modes of buffalo PGRP1 receptor complexed with meso-diaminopimelic acid and lysine-type peptidoglycans by molecular dynamics simulation and free energy calculation. Chem Biol Interact 2014; 220:255-68. [PMID: 25014416 DOI: 10.1016/j.cbi.2014.06.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 05/28/2014] [Accepted: 06/30/2014] [Indexed: 12/20/2022]
Abstract
The peptidoglycan recognition proteins (PGRPs) are the key components of innate-immunity, and are highly specific for the recognition of bacterial peptidoglycans (PGN). Among different mammalian PGRPs, the PGRP1 binds to murein PGN of Gram-positive bacteria (lysine-type) and also have bactericidal activity towards Gram-negative bacteria (diaminopimelic acid or Dap-type). Buffaloes are the major sources of milk and meat in Asian sub-continents and are highly exposed to bacterial infections. The PGRP activates the innate-immune signaling, but their studies has been confined to limited species due to lack of structural and functional information. So, to understand the structural constituents, 3D model of buffalo PGRP1 (bfPGRP1) was constructed and conformational and dynamics properties of bfPGRP1 was studied. The bfPGRP1 model highly resembled human and camel PGRP structure, and shared a highly flexible N-terminus and centrally placed L-shaped cleft. Docking simulation of muramyl-tripeptide, tetrapeptide, pentapeptide-Dap-(MTP-Dap, MTrP-Dap and MPP-Dap) and lysine-type (MTP-Lys, MTrP-Lys and MPP-Lys) in AutoDock 4.2 and ArgusLab 4.0.1 anticipated β1, α2, α4, β4, and loops connecting β1-α2, α2-β2, β3-β4 and α4-α5 as the key interacting domains. The bfPGRP1-ligand complex molecular dynamics simulation followed by free binding energy (BE) computation conceded BE values of -18.30, -35.53, -41.80, -25.03, -24.62 and -22.30 kJ mol(-1) for MTP-Dap, MTrP-Dap, MPP-Dap, MTP-Lys, MTrP-Lys and MPP-Lys, respectively. The groove-surface and key binding residues involved in PGN-Dap and Lys-type interaction intended by the molecular docking, and were also accompanied by significant BE values directed their importance in pharmacogenomics, and warrants further in vivo studies for drug targeting and immune signaling pathways exploration.
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Affiliation(s)
- Bikash Ranjan Sahoo
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India; Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, Osaka Prefecture 5650871, Japan.
| | - Praveen Kumar Dubey
- Immunology Frontier Research Centre, Osaka University, Osaka Prefecture 5650871, Japan.
| | - Shubham Goyal
- RIKEN Center for Life Science Technologies, Yokohama 2300045, Japan
| | - Gopal Krushna Bhoi
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India
| | - Santosh Kumar Lenka
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India
| | - Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India; Biotechnology Laboratory, Central Inland Fisheries Research Institute, Kolkata, West Bengal 700120, India
| | - Sukanta Kumar Pradhan
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India
| | - Ranjit Singh Kataria
- Division of Animal Biotechnology, National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
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