1
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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: 25] [Impact Index Per Article: 6.3] [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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Barletta GP, Franchini G, Corsico B, Fernandez-Alberti S. Fatty Acid and Retinol-Binding Protein: Unusual Protein Conformational and Cavity Changes Dictated by Ligand Fluctuations. J Chem Inf Model 2019; 59:3545-3555. [PMID: 31365253 DOI: 10.1021/acs.jcim.9b00364] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Lipid-binding proteins (LBPs) are soluble proteins responsible for the uptake, transport, and storage of a large variety of hydrophobic lipophilic molecules including fatty acids, steroids, and other lipids in the cellular environment. Among the LBPs, fatty acid binding proteins (FABPs) present preferential binding affinities for long-chain fatty acids. While most of FABPs in vertebrates and invertebrates present similar β-barrel structures with ligands accommodated in their central cavity, parasitic nematode worms exhibit additional unusual α-helix rich fatty acid- and retinol-binding proteins (FAR). Herein, we report the comparison of extended molecular dynamics (MD) simulations performed on the ligand-free and palmitic acid-bond states of the Necator americanus FAR-1 (Na-FAR-1) with respect to other classical β-barrel FABPs. Principal component analysis (PCA) has been used to identify the different conformations adopted by each system during MD simulations. The α-helix fold encompasses a complex internal ligand-binding cavity with a remarkable conformational plasticity that allows reversible switching between distinct states in the holo-Na-FAR-1. The cavity can change up to one-third of its size affected by conformational changes of the protein-ligand complex. Besides, the ligand inside the cavity is not fixed but experiences large conformational changes between bent and stretched conformations. These changes in the ligand conformation follow changes in the cavity size dictated by the transient protein conformation. On the contrary, protein-ligand complex in β-barrel FABPs fluctuates around a unique conformation. The significantly more flexible holo-Na-FAR-1 ligand-cavity explains its larger ligand multiplicity respect to β-barrel FABPs.
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Affiliation(s)
- G P Barletta
- Universidad Nacional de Quilmes/CONICET , Roque Saenz Peña 352 , B1876BXD Bernal , Argentina
| | - G Franchini
- Instituto de Investigaciones Bioquímicas de La Plata , CONICET-UNLP, Facultad de Ciencias Médicas , calles 60 y 120 s/n , 1900 La Plata , Argentina
| | - B Corsico
- Instituto de Investigaciones Bioquímicas de La Plata , CONICET-UNLP, Facultad de Ciencias Médicas , calles 60 y 120 s/n , 1900 La Plata , Argentina
| | - S Fernandez-Alberti
- Universidad Nacional de Quilmes/CONICET , Roque Saenz Peña 352 , B1876BXD Bernal , Argentina
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3
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Cheng P, Liu D, Chee PX, Yang D, Long D. Atomistic Insights into the Functional Instability of the Second Helix of Fatty Acid Binding Protein. Biophys J 2019; 117:239-246. [PMID: 31301805 DOI: 10.1016/j.bpj.2019.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/19/2019] [Accepted: 06/13/2019] [Indexed: 12/21/2022] Open
Abstract
Structural dynamics of fatty acid binding proteins (FABPs), which accommodate poorly soluble ligands in the internalized binding cavities, are intimately related to their function. Recently, local unfolding of the α-helical cap in a variant of human intestinal FABP (IFABP) has been shown to correlate with the kinetics of ligand association, shedding light on the nature of the critical conformational reorganization. Yet, the physical origin and mechanism of the functionally relevant transient unfolding remain elusive. Here, we investigate the intrinsic structural instability of the second helix (αII) of IFABP in comparison with other segments of the protein using hydrogen-exchange NMR spectroscopy, microsecond molecular dynamics simulations, and enhanced sampling techniques. Although tertiary interactions positively contribute to the stability of helices in IFABP, the intrinsic unfolding tendency of αII is encoded in its primary sequence and can be described by the Lifson-Roig theory in the absence of tertiary interactions. The unfolding pathway of αII in intact proteins involves an on-pathway intermediate state that is characterized with the fraying of the last helical turn, captured by independent enhanced sampling methods. The simulations in this work, combined with hydrogen-exchange NMR data, provide new, to our knowledge, atomistic insights into the functional local unfolding of FABPs.
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Affiliation(s)
- Peng Cheng
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Dan Liu
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Pin Xuan Chee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Dong Long
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China; Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, China.
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4
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Li Y, Li X, Dong Z. Concerted dynamic motions of an FABP4 model and its ligands revealed by microsecond molecular dynamics simulations. Biochemistry 2014; 53:6409-17. [PMID: 25231537 PMCID: PMC4196735 DOI: 10.1021/bi500374t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
In this work, we investigate the
dynamic motions of fatty acid
binding protein 4 (FABP4) in the absence and presence of a ligand
by explicitly solvated all-atom molecular dynamics simulations. The
dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is
compared via multiple 1.2 μs simulations. In our simulations,
the protein interconverts between the open and closed states. Ligand-free
FABP4 prefers the closed state, whereas ligand binding induces a conformational
transition to the open state. Coupled with opening and closing of
FABP4, the ligand adopts distinct binding modes, which are identified
and compared with crystal structures. The concerted dynamics of protein
and ligand suggests that there may exist multiple FABP4–ligand
binding conformations. Thus, this work provides details about how
ligand binding affects the conformational preference of FABP4 and
how ligand binding is coupled with a 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, United States
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5
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Esteves A, Paulino Zunini M. In silicostudies ofEchinococcus granulosusFABPs. J Biomol Struct Dyn 2013; 31:224-39. [DOI: 10.1080/07391102.2012.698246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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6
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Majava V, Polverini E, Mazzini A, Nanekar R, Knoll W, Peters J, Natali F, Baumgärtel P, Kursula I, Kursula P. Structural and functional characterization of human peripheral nervous system myelin protein P2. PLoS One 2010; 5:e10300. [PMID: 20421974 PMCID: PMC2858655 DOI: 10.1371/journal.pone.0010300] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 03/24/2010] [Indexed: 11/19/2022] Open
Abstract
The myelin sheath is a tightly packed multilayered membrane structure insulating selected axons in the central and the peripheral nervous systems. Myelin is a biochemically unique membrane, containing a specific set of proteins. In this study, we expressed and purified recombinant human myelin P2 protein and determined its crystal structure to a resolution of 1.85 A. A fatty acid molecule, modeled as palmitate based on the electron density, was bound inside the barrel-shaped protein. Solution studies using synchrotron radiation indicate that the crystal structure is similar to the structure of the protein in solution. Docking experiments using the high-resolution crystal structure identified cholesterol, one of the most abundant lipids in myelin, as a possible ligand for P2, a hypothesis that was proven by fluorescence spectroscopy. In addition, electrostatic potential surface calculations supported a structural role for P2 inside the myelin membrane. The potential membrane-binding properties of P2 and a peptide derived from its N terminus were studied. Our results provide an enhanced view into the structure and function of the P2 protein from human myelin, which is able to bind both monomeric lipids inside its cavity and membrane surfaces.
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Affiliation(s)
- Viivi Majava
- Department of Biochemistry, University of Oulu, Oulu, Finland
| | | | | | - Rahul Nanekar
- Department of Biochemistry, University of Oulu, Oulu, Finland
| | - Wiebke Knoll
- Institut Laue-Langevin, Grenoble, France
- University Joseph Fourier, Grenoble, France
| | - Judith Peters
- Institut Laue-Langevin, Grenoble, France
- University Joseph Fourier, Grenoble, France
- Institut de Biologie Structurale, Grenoble, France
| | - Francesca Natali
- Institut Laue-Langevin, Grenoble, France
- Consiglio Nazionale delle Richerche – Operative Group in Grenoble, Grenoble, France
| | | | - Inari Kursula
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Electron Synchrotron, University of Hamburg, Hamburg, Germany
| | - Petri Kursula
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Electron Synchrotron, University of Hamburg, Hamburg, Germany
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7
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Insight into the interaction sites between fatty acid binding proteins and their ligands. J Mol Model 2009; 16:929-38. [DOI: 10.1007/s00894-009-0599-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 09/20/2009] [Indexed: 10/20/2022]
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8
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Ricchiuto P, Rocco AG, Gianazza E, Corrada D, Beringhelli T, Eberini I. Structural and dynamic roles of permanent water molecules in ligand molecular recognition by chicken liver bile acid binding protein. J Mol Recognit 2008; 21:348-54. [DOI: 10.1002/jmr.908] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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Mihajlovic M, Lazaridis T. Modeling fatty acid delivery from intestinal fatty acid binding protein to a membrane. Protein Sci 2007; 16:2042-55. [PMID: 17660261 PMCID: PMC2206986 DOI: 10.1110/ps.072875307] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Intestinal fatty acid binding protein (IFABP) interacts with biological membranes and delivers fatty acid (FA) into them via a collisional mechanism. However, the membrane-bound structure of the protein and the pathway of FA transfer are not precisely known. We used molecular dynamics (MD) simulations with an implicit membrane model to determine the optimal orientation of apo- and holo-IFABP (bound with palmitate) on an anionic membrane. In this orientation, the helical portal region, delimited by the alphaII helix and the betaC-betaD and betaE-betaF turns, is oriented toward the membrane whereas the putative beta-strand portal, delimited by the betaB-betaC, betaF-betaG, betaH-betaI turns and the N terminus, is exposed to solvent. Starting from the MD structure of holo-IFABP in the optimal orientation relative to the membrane, we examined the release of palmitate via both pathways. Although the domains can widen enough to allow the passage of palmitate, fatty acid release through the helical portal region incurs smaller conformational changes and a lower energetic cost.
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Affiliation(s)
- Maja Mihajlovic
- Department of Chemistry, City College of New York/CUNY, New York, New York 10031, USA
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10
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Ravindranath MH, Yesowitch P, Sumobay C, Morton DL. Glycoimmunomics of human cancer: current concepts and future perspectives. Future Oncol 2007; 3:201-14. [PMID: 17381420 DOI: 10.2217/14796694.3.2.201] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Future strategies for the treatment of human cancer require a full appreciation of the intracellular and extracellular changes that accompany neoplastic transformation. The changes may involve a variety of micro- and macro-molecules, including, but not restricted to, peptides, proteins (with sugar and/or lipid moieties), oligosaccharides, glycolipids (neutral or acidic, e.g., gangliosides), ceramides, fatty acids and other lipids. Although several therapeutic approaches have been well developed in recent years, most of the reported studies focus on proteins and peptides. Glycoantigens and lipoantigens have been neglected. Elucidation of the profiles and properties of all molecules associated with tumor progression is required to develop a successful strategy to treat human cancer. This review describes the unique immunomics of tumor-associated glycoantigens and explains why the field of glycoimmunomics may yield clinically important biomarkers and treatments for the management of human cancer.
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Affiliation(s)
- Mepur H Ravindranath
- Department of Glycoimmunotherapy, John Wayne Cancer Institute, Saint John's Health Center, Santa Monica, CA 90404-2302, USA.
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11
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Polverini E, Fornabaio M, Fasano A, Carlone G, Riccio P, Cavatorta P. The pH-dependent unfolding mechanism of P2 myelin protein: an experimental and computational study. J Struct Biol 2005; 153:253-63. [PMID: 16427315 DOI: 10.1016/j.jsb.2005.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 11/04/2005] [Accepted: 11/10/2005] [Indexed: 10/25/2022]
Abstract
The P2 protein is a small, extrinsic protein of the myelin membrane in the peripheral nervous system that structurally belongs to the fatty acid binding proteins (FABPs) family, sharing with them a 10 strands beta-barrel structure. FABPs appear to be involved in cellular fatty acid transport, but very little is known about the role of P2 in the metabolism of peripheral myelin lipids. Study of protein conformation at different pHs is a useful tool for the characterization of the unfolding mechanisms and the intrinsic conformational properties of the protein, and may give insight into factors that guide protein folding pathways. In particular, low pH conditions have been shown to induce partially folded states in several proteins. In this paper, the acidic unfolding of purified P2 protein was studied with both spectroscopic techniques and molecular dynamics simulation. Both experimental and computational results indicate the presence of a partly folded state at low pH, which shows structural changes mainly involving the lid that is formed by the helix-turn-helix domain. The opening of the lid, together with a barrel relaxation, could regulate the ligand exchanges near the cell membrane, supporting the hypothesis that the P2 protein may transport fatty acids between Schwann cells and peripheral myelin.
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Affiliation(s)
- Eugenia Polverini
- Dipartimento di Fisica, CNR-INFM and CNISM, Università di Parma, Parco Area delle Scienze, 7/A, 43100 Parma, Italy.
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12
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Friedman R, Nachliel E, Gutman M. Fatty acid binding proteins: same structure but different binding mechanisms? Molecular dynamics simulations of intestinal fatty acid binding protein. Biophys J 2005; 90:1535-45. [PMID: 16361342 PMCID: PMC1367305 DOI: 10.1529/biophysj.105.071571] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fatty acid binding proteins (FABPs) carry fatty acids (FAs) and other lipids in the cellular environment, and are thus involved in processes such as FA uptake, transport, and oxidation. These proteins bind either one or two ligands in a binding site, which appears to be inaccessible from the bulk. Thus, the entry of the substrate necessitates a conformational change, whose nature is still unknown. A possible description of the ligand binding process is given by the portal hypothesis, which suggests that the FA enters the protein through a dynamic area known as the portal region. On the other hand, recent simulations of the adipocyte lipid binding protein (ALBP) suggested a different entry site (the alternative portal). In this article, we discuss molecular dynamics simulations of the apo-intestinal-FABP (I-FABP) in the presence of palmitate molecule(s) in the simulation box. The simulations were carried out to study whether the FA can enter the protein during the simulations (as in the ALBP) and where the ligand entry site is (the portal region, the alternative portal or a different domain). The analysis of the simulations revealed a clear difference between the ALBP and the I-FABP. In the latter case, the palmitate preferentially adsorbed to the portal region, which was more mobile than the rest of the protein. However, no ligand entry was observed in the multi-nanosecond-long simulations, in contrast to ALBP. These findings suggest that, although the main structural motif of the FABPs is common, the fine details of each individual protein structure grossly modulate its reactivity.
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Affiliation(s)
- Ran Friedman
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
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13
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Bakowies D, van Gunsteren WF. Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water. J Mol Biol 2002; 315:713-36. [PMID: 11812142 DOI: 10.1006/jmbi.2001.5202] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two molecular dynamics simulations of 5 ns each have been carried out for rat intestinal fatty acid binding protein, in apo-form and with bound palmitate. The fatty acid and a number of water molecules are encapsulated in a large interior cavity of the barrel-shaped protein. The simulations are compared to experimental data and analyzed in terms of root mean square deviations, atomic B-factors, secondary structure elements, hydrogen bond patterns, and distance constraints derived from nuclear Overhauser experiments. Excellent agreement is found between simulated and experimental solution structures of holo-FABP, but a number of differences are observed for the apo-form. The ligand in holo-FABP shows considerable displacement after about 1.5 ns and displays significant configurational entropy. A novel computational approach has been employed to identify internal water and to capture exchange pathways. Orifices in the portal and gap regions of the protein, discussed in the experimental literature, have been confirmed as major openings for solvent exchange between the internal cavity and bulk water. A third opening on the opposite side of the barrel experiences significant exchange but it does not provide a pathway for further passage to the central cavity. Internal water is characterized in terms of density distributions, interaction energies, mobility, protein contact times, and water molecule coordination. A number of differences are observed between the apo and holo-forms and related to differences in the protein structure. Solvent inside apo-FABP, for example, shows characteristics of a water droplet, while solvent in holo-FABP benefits from interactions with the ligand headgroup and slightly stronger interactions with protein residues.
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Affiliation(s)
- Dirk Bakowies
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zürich, 8093, Switzerland.
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14
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Abstract
Muscle or heart fatty acid-binding protein is a low molecular weight protein that binds long-chain fatty acids in the cytosol of muscle tissues. The three-dimensional structure of the human, bovine and insect proteins are known, either via X-ray or NMR techniques. The folding of the protein closely resembles that of the other FABPs: ten anti-parallel beta-strands are arranged to form a clam shell, closed at one end by two alpha-helices. This arrangement allows the formation of an internal cavity where the fatty acid can be accommodated, protected and isolated from the external environment. The fatty acid in the protein interior is stabilized by electrostatic and hydrogen bond interactions of its carboxylic head with charged or polar residues of the protein and by interactions of its tail with hydrophobic residues. The three-dimensional structure of different fatty acid-protein complexes along with molecular dynamics simulations are now providing insight into the molecular details of the specificity of the ligand binding.
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Affiliation(s)
- G Zanotti
- Dipartimento Chimica Organica, Università di Padova e Centro Studi Biopolimeri del CNR, Via Marzolo 1, 35131, Padova, Italy
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15
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Reese-Wagoner A, Thompson J, Banaszak L. Structural properties of the adipocyte lipid binding protein. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1441:106-16. [PMID: 10570239 DOI: 10.1016/s1388-1981(99)00154-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The adipocyte lipid binding protein, ALBP (also adipocyte fatty acid binding protein, A-FABP, 422 protein, aP2, and p15 protein), is one of the most studied of the intracellular lipid binding protein family. Here we sequentially compare the different sources of ALBP and describe the idea that one-third of the amino acid side chains near the N-terminal end appear to play a major role in conformational dynamics and in ligand transfer. Crystallographic data for mouse ALBP are summarized and the ligand binding cavity analyzed in terms of the overall surface and conformational dynamics. The region of the proposed ligand portal is described. Amino acid side chains critical to cavity formation and fatty acid interactions are analyzed by comparing known crystal structures containing a series of different hydrophobic ligands. Finally, we address ALBP ligand binding affinity and thermodynamic studies.
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Affiliation(s)
- A Reese-Wagoner
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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16
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Woolf TB. Simulations of fatty acid-binding proteins suggest sites important for function. I. Stearic acid. Biophys J 1998; 74:681-93. [PMID: 9533682 PMCID: PMC1302550 DOI: 10.1016/s0006-3495(98)73994-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Molecular dynamics simulations of two structurally similar fatty acid-binding proteins interacting with stearic acid are described. The calculations relate to recent ligand binding measurements and suggest similarities and differences between the two systems. Charged and neutral forms of the fatty acid were examined. The charged forms led to rapid trajectory divergence, whereas the protonated forms remained stable over the length of their 1-ns production trajectories. The two protein systems showed similar sets of total interaction energies with the ligand. However, the strengths of individual amino acids interacting with the ligand differ. Furthermore, covariance analysis of the ligand with both protein and water suggests that the stearic acid in the adipocyte fatty acid-binding protein is coupled more strongly to the water than to the protein. The stearic acid in the muscle fatty acid-binding protein is seen to be coupled differentially along the length of the chain to the protein. These differences could help to rationalize the stronger binding affinity for stearic acid in the human muscle fatty acid-binding protein. An importance scale, based on both covariance and interaction energy with the ligand, is proposed to identify residues that may be important for binding function.
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Affiliation(s)
- T B Woolf
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
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17
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Abstract
Brain lipid-binding protein (BLBP) is a member of the fatty acid-binding protein (FABP) family. Although BLBP expression in the developing central nervous system is complex, a close correlation between its expression and radial glial differentiation has been observed. Furthermore, antibodies to BLBP can block glial cell differentiation in mixed primary cell cultures. Here we describe the ligand binding properties of BLBP. The binding affinities of BLBP for oleic acid (Kd approximately 0.44 microM) and arachidonic acid (Kd approximately 0.25 microM) are similar to those reported for other FABPs, but BLBP does not bind to palmitic acid or arachidinic acid. These and other experiments establish that BLBP has a strong preference for binding long chain polyunsaturated fatty acids. A probable in vivo ligand for BLBP is docosahexaenoic acid (DHA), since its binding affinity (Kd approximately 10 nM) is the highest yet reported for an FABP/ligand interaction, exceeding even the affinity of retinoic acid for its binding proteins. Furthermore, the requirement of DHA for nervous system development and the coincident expression of BLBP during these developmental stages suggest that the physiologic role of BLBP may involve DHA utilization. Finally, we present a structural model of BLBP/DHA interaction that provides insight into both the structural characteristics important for ligand binding and the effects of specific mutations upon BLBP/ligand interactions.
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Affiliation(s)
- L Z Xu
- Howard Hughes Medical Institute, Laboratory of Molecular Biology, The Rockefeller University, New York, New York 10021-6399, USA
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Glatz JF, van der Vusse GJ. Cellular fatty acid-binding proteins: their function and physiological significance. Prog Lipid Res 1996; 35:243-82. [PMID: 9082452 DOI: 10.1016/s0163-7827(96)00006-9] [Citation(s) in RCA: 366] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- J F Glatz
- Department of Physiology, Maastricht University, The Netherlands.
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