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Espinosa YR, Alvarez HA, Howard EI, Carlevaro CM. Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment. J Biomol Struct Dyn 2020; 39:3459-3468. [PMID: 32448092 DOI: 10.1080/07391102.2020.1773315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the macromolecules and explore the microstates that the confined proteins can adopt in the crystalline network. We explored different strategies to simulate a heart fatty acid binding protein (H-FABP) crystal by means of Molecular Dynamics (MD) simulations. We evaluate the effect of introducing restraints according to experimental isotropic B-factors and we analyzed the H-FABP motions in the crystal using Principal Component Analysis (PCA), isotropic and anisotropic B-factors. We compared the behavior of the protein simulated in the crystal confinement versus in solution, and we observed the effect of that confinement in the mobility of the protein residues. Restraining one-third of Cα atoms based on experimental B-factors produce lower B-factors than simulations without restraints, showing that the position restraint of the atoms with the lowest experimental B-factor is a good strategy to maintain the geometry of the crystal with an obvious decrease in the degrees of motion of the protein. PCA shows that, as position restraint reduces the conformational space explored by the system, the motion of the crystal is better recovered, for an essential subspace of the same size, in the simulations without restraints. Restraining only one Cα seems to be a good balance between giving flexibility to the system and preserving its structure. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yanis R Espinosa
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), La Plata, Argentina.,Grupo de Bioquímica Teórica, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - H Ariel Alvarez
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), La Plata, Argentina.,Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, UNLP, La Plata, Argentina.,Instituto de Ciencias de la Salud, Universidad Nacional Arturo Jauretche, Buenos Aires, Argentina
| | - Eduardo I Howard
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), La Plata, Argentina.,Universidad Tecnológica Nacional- Facultad Regional Tierra del Fuego, Ushuaia, Tierra del Fuego, Argentina
| | - C Manuel Carlevaro
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), La Plata, Argentina.,Departamento de Ingeniería Mecánica, Universidad Tecnológica Nacional, Facultad Regional La Plata, La Plata, Argentina
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2
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Lamas Bervejillo M, Bonanata J, Franchini GR, Richeri A, Marqués JM, Freeman BA, Schopfer FJ, Coitiño EL, Córsico B, Rubbo H, Ferreira AM. A FABP4-PPARγ signaling axis regulates human monocyte responses to electrophilic fatty acid nitroalkenes. Redox Biol 2020; 29:101376. [PMID: 31926616 PMCID: PMC6926352 DOI: 10.1016/j.redox.2019.101376] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/14/2019] [Accepted: 11/06/2019] [Indexed: 02/07/2023] Open
Abstract
Nitro-fatty acids (NO2-FA) are electrophilic lipid mediators derived from unsaturated fatty acid nitration. These species are produced endogenously by metabolic and inflammatory reactions and mediate anti-oxidative and anti-inflammatory responses. NO2-FA have been postulated as partial agonists of the Peroxisome Proliferator-Activated Receptor gamma (PPARγ), which is predominantly expressed in adipocytes and myeloid cells. Herein, we explored molecular and cellular events associated with PPARγ activation by NO2-FA in monocytes and macrophages. NO2-FA induced the expression of two PPARγ reporter genes, Fatty Acid Binding Protein 4 (FABP4) and the scavenger receptor CD36, at early stages of monocyte differentiation into macrophages. These responses were inhibited by the specific PPARγ inhibitor GW9662. Attenuated NO2-FA effects on PPARγ signaling were observed once cells were differentiated into macrophages, with a significant but lower FABP4 upregulation, and no induction of CD36. Using in vitro and in silico approaches, we demonstrated that NO2-FA bind to FABP4. Furthermore, the inhibition of monocyte FA binding by FABP4 diminished NO2-FA-induced upregulation of reporter genes that are transcriptionally regulated by PPARγ, Keap1/Nrf2 and HSF1, indicating that FABP4 inhibition mitigates NO2-FA signaling actions. Overall, our results affirm that NO2-FA activate PPARγ in monocytes and upregulate FABP4 expression, thus promoting a positive amplification loop for the downstream signaling actions of this mediator.
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Affiliation(s)
- M Lamas Bervejillo
- Laboratorio de Inmunología, Instituto de Higiene, Facultad de Ciencias/Facultad de Química, Universidad de la República (UdelaR), Montevideo, CP 11600, Uruguay
| | - J Bonanata
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, UdelaR, Montevideo, CP 11400, Uruguay; Centro de Investigaciones Biomédicas (CeInBio), UdelaR, Montevideo, CP 11800, Uruguay
| | - G R Franchini
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - A Richeri
- Laboratorio de Biología Celular, Departamento de Neurofarmacología Experimental, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, CP 11600, Uruguay
| | - J M Marqués
- Laboratorio de Investigación en Vacunas, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, UdelaR, Montevideo, CP 11600, Uruguay
| | - B A Freeman
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - F J Schopfer
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - E L Coitiño
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, UdelaR, Montevideo, CP 11400, Uruguay; Centro de Investigaciones Biomédicas (CeInBio), UdelaR, Montevideo, CP 11800, Uruguay.
| | - B Córsico
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - H Rubbo
- Centro de Investigaciones Biomédicas (CeInBio), UdelaR, Montevideo, CP 11800, Uruguay; Departamento de Bioquímica, Facultad de Medicina, UdelaR, Montevideo, CP 11800, Uruguay
| | - A M Ferreira
- Laboratorio de Inmunología, Instituto de Higiene, Facultad de Ciencias/Facultad de Química, Universidad de la República (UdelaR), Montevideo, CP 11600, Uruguay.
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Dash R, Ali MC, Dash N, Azad MAK, Hosen SMZ, Hannan MA, Moon IS. Structural and Dynamic Characterizations Highlight the Deleterious Role of SULT1A1 R213H Polymorphism in Substrate Binding. Int J Mol Sci 2019; 20:ijms20246256. [PMID: 31835852 PMCID: PMC6969939 DOI: 10.3390/ijms20246256] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 12/16/2022] Open
Abstract
Sulfotransferase 1A1 (SULT1A1) is responsible for catalyzing various types of endogenous and exogenous compounds. Accumulating data indicates that the polymorphism rs9282861 (R213H) is responsible for inefficient enzymatic activity and associated with cancer progression. To characterize the detailed functional consequences of this mutation behind the loss-of-function of SULT1A1, the present study deployed molecular dynamics simulation to get insights into changes in the conformation and binding energy. The dynamics scenario of SULT1A1 in both wild and mutated types as well as with and without ligand showed that R213H induced local conformational changes, especially in the substrate-binding loop rather than impairing overall stability of the protein structure. The higher conformational changes were observed in the loop3 (residues, 235-263), turning loop conformation to A-helix and B-bridge, which ultimately disrupted the plasticity of the active site. This alteration reduced the binding site volume and hydrophobicity to decrease the binding affinity of the enzyme to substrates, which was highlighted by the MM-PBSA binding energy analysis. These findings highlight the key insights of structural consequences caused by R213H mutation, which would enrich the understanding regarding the role of SULT1A1 mutation in cancer development and also xenobiotics management to individuals in the different treatment stages.
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Affiliation(s)
- Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea
| | - Md Chayan Ali
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - Nayan Dash
- Department of Computer Science and Engineering, BGC Trust University, Bangladesh, Chittagong 4381, Bangladesh
| | - Md Abul Kalam Azad
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - S M Zahid Hosen
- Pancreatic Research Group, South Western Sydney Clinical School, University of New South Wales, and Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Md Abdul Hannan
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea
- Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Il Soo Moon
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea
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New insights in the opening mechanism of the heart-type fatty acid binding protein in its apo form (apo-FABP3). Struct Chem 2019. [DOI: 10.1007/s11224-019-01446-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Wu W, Han L, Wang C, Wen X, Sun H, Yuan H. Structural insights into ligand binding features of dual FABP4/5 inhibitors by molecular dynamics simulations. J Biomol Struct Dyn 2019; 37:4790-4800. [PMID: 30590992 DOI: 10.1080/07391102.2018.1561328] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The fatty acid binding protein (FABP) 4 and 5 have been considered as potential targets for the treatment of metabolic diseases. A compensatory upregulation of FABP5 due to the gene ablation of FABP4 in adipocytes indicated the importance of dual FABP4/5 inhibitors. A few compounds have been discovered as dual FABP4/5 inhibitors. However, none exhibited equivalent inhibitory activity against both FABP4 and FABP5, and almost all compounds showed weaker inhibition against FABP5. To provide a better structural understanding for the design of potent dual FABP4/5 inhibitors, molecular dynamics simulations have been performed for 100 ns to disclose the ligand binding features in FABP4 and FABP5 using Amber14, respectively. Key residues were identified by analysis of close contact, hydrogen bond occupancy, binding free energy and alanine scanning mutagenesis. In addition, induced-fit effects have been observed upon ligand binding in the process of simulations. The shifted alkyl chain of ligand in FABP4 was significantly different from that in FABP5 due to the corresponding residues (Phe58FABP4 and Leu60FABP5). Thus, to avoid different steric effects made by these two residues, hydrophobic groups of suitable size should be taken into account. Besides, electrostatic and steric effects with Arg107FABP4 and Arg109FABP5 should be paid more attention to. The results will facilitate the rational design of dual FABP4/5 inhibitors.
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Affiliation(s)
- Wenzhen Wu
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University , Nanjing , P.R. China
| | - Lishuai Han
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University , Nanjing , P.R. China
| | - Chaoxin Wang
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University , Nanjing , P.R. China
| | - Xiaoan Wen
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University , Nanjing , P.R. China
| | - Hongbin Sun
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University , Nanjing , P.R. China
| | - Haoliang Yuan
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University , Nanjing , P.R. China
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Yan F, Liu X, Zhang S, Su J, Zhang Q, Chen J. Molecular Dynamics Exploration of Selectivity of Dual Inhibitors 5M7, 65X, and 65Z toward Fatty Acid Binding Proteins 4 and 5. Int J Mol Sci 2018; 19:ijms19092496. [PMID: 30142969 PMCID: PMC6164837 DOI: 10.3390/ijms19092496] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/14/2018] [Accepted: 08/18/2018] [Indexed: 12/11/2022] Open
Abstract
Designing highly selective inhibitors of fatty acid binding proteins 4 and 5 (FABP4 and FABP5) is of importance for treatment of some diseases related with inflammation, metabolism, and tumor growth. In this study, molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were performed to probe binding selectivity of three inhibitors (5M7, 65X, and 65Z) to FABP4/FABP5 with Ki values of 0.022/0.50 μM, 0.011/0.086 μM, and 0.016/0.12 μM, respectively. The results not only suggest that all inhibitors associate more tightly with FABP4 than FABP5, but also prove that the main forces driving the selective bindings of inhibitors to FABP4 and FABP5 stem from the difference in the van der Waals interactions and polar interactions of inhibitors with two proteins. Meanwhile, a residue-based free energy decomposition method was applied to reveal molecular basis that inhibitors selectively interact with individual residues of two different proteins. The calculated results show that the binding difference of inhibitors to the residues (Phe16, Phe19), (Ala33, Gly36), (Phe57, Leu60), (Ala75, Ala78), (Arg126, Arg129), and (Tyr128, Tyr131) in (FABP4, FABP5) drive the selectivity of inhibitors toward FABP4 and FABP5. This study will provide great help for further design of effective drugs to protect against a series of metabolic diseases, arteriosclerosis, and inflammation.
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Affiliation(s)
- Fangfang Yan
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Jing Su
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China.
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7
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Hunter NH, Bakula BC, Bruce CD. Molecular dynamics simulations of apo and holo forms of fatty acid binding protein 5 and cellular retinoic acid binding protein II reveal highly mobile protein, retinoic acid ligand, and water molecules. J Biomol Struct Dyn 2017; 36:1893-1907. [PMID: 28566049 DOI: 10.1080/07391102.2017.1337591] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Structural and dynamic properties from a series of 300 ns molecular dynamics, MD, simulations of two intracellular lipid binding proteins, iLBPs, (Fatty Acid Binding Protein 5, FABP5, and Cellular Retinoic Acid Binding Protein II, CRABP-II) in both the apo form and when bound with retinoic acid reveal a high degree of protein and ligand flexibility. The ratio of FABP5 to CRABP-II in a cell may determine whether it undergoes natural apoptosis or unrestricted cell growth in the presence of retinoic acid. As a result, FABP5 is a promising target for cancer therapy. The MD simulations presented here reveal distinct differences in the two proteins and provide insight into the binding mechanism. CRABP-II is a much larger, more flexible protein that closes upon ligand binding, where FABP5 transitions to an open state in the holo form. The traditional understanding obtained from crystal structures of the gap between two β-sheets of the β-barrel common to iLBPs and the α-helix cap that forms the portal to the binding pocket is insufficient for describing protein conformation (open vs. closed) or ligand entry and exit. When the high degree of mobility between multiple conformations of both the ligand and protein are examined via MD simulation, a new mode of ligand motion that improves understanding of binding dynamics is revealed.
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Affiliation(s)
- Nathanael H Hunter
- a Department of Chemistry , John Carroll University , University Heights , OH , USA
| | - Blair C Bakula
- a Department of Chemistry , John Carroll University , University Heights , OH , USA
| | - Chrystal D Bruce
- a Department of Chemistry , John Carroll University , University Heights , OH , USA
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Li Y, Li X, Dong Z. Exploration of gated ligand binding recognizes an allosteric site for blocking FABP4-protein interaction. Phys Chem Chem Phys 2016; 17:32257-67. [PMID: 26580122 DOI: 10.1039/c5cp04784f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fatty acid binding protein 4 (FABP4), reversibly binding to fatty acids and other lipids with high affinities, is a potential target for treatment of cancers. The binding site of FABP4 is buried in an interior cavity and thereby ligand binding/unbinding is coupled with opening/closing of FABP4. It is a difficult task both experimentally and computationally to illuminate the entry or exit pathway, especially with the conformational gating. In this report we combine extensive computer simulations, clustering analysis, and the Markov state model to investigate the binding mechanism of FABP4 and troglitazone. Our simulations capture spontaneous binding and unbinding events as well as the conformational transition of FABP4 between the open and closed states. An allosteric binding site on the protein surface is recognized for the development of novel FABP4 inhibitors. The binding affinity is calculated and compared with the experimental value. The kinetic analysis suggests that ligand residence on the protein surface may delay the binding process. Overall, our results provide a comprehensive picture of ligand diffusion on the protein surface, ligand migration into the buried cavity, and the conformational change of FABP4 at an atomic level.
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Affiliation(s)
- Yan Li
- The Hormel Institute, University of Minnesota, Austin Minnesota 55912, USA.
| | - Xiang Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, 450001 Zhengzhou, Henan, China
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin Minnesota 55912, USA.
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Li Y, Dong Z. Effect of Clustering Algorithm on Establishing Markov State Model for Molecular Dynamics Simulations. J Chem Inf Model 2016; 56:1205-15. [DOI: 10.1021/acs.jcim.6b00181] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yan Li
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
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