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Chen S, Pan Z, Liu M, Guo L, Jiang X, He G. Recent Advances on Small-Molecule Inhibitors of Lipocalin-like Proteins. J Med Chem 2024; 67:5144-5167. [PMID: 38525852 DOI: 10.1021/acs.jmedchem.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Lipid transfer proteins (LTPs) are crucial players in nonvesicular lipid trafficking. LTPs sharing a lipocalin lipid transfer domain (lipocalin-like proteins) have a wide range of biological functions, such as regulating immune responses and cell proliferation, differentiation, and death as well as participating in the pathogenesis of inflammatory, metabolic, and neurological disorders and cancer. Therefore, the development of small-molecule inhibitors targeting these LTPs is important and has potential clinical applications. Herein, we summarize the structure and function of lipocalin-like proteins, mainly including retinol-binding proteins, lipocalins, and fatty acid-binding proteins and discuss the recent advances on small-molecule inhibitors for these protein families and their applications in disease treatment. The findings of our Perspective can provide guidance for the development of inhibitors of these LTPs and highlight the challenges that might be faced during the procedures.
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Affiliation(s)
- Siliang Chen
- Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhaoping Pan
- Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mingxia Liu
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Linghong Guo
- Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xian Jiang
- Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Gu He
- Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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Alvarez HA, Cousido-Siah A, Espinosa YR, Podjarny A, Carlevaro CM, Howard E. Lipid exchange in crystal-confined fatty acid binding proteins: X-ray evidence and molecular dynamics explanation. Proteins 2023; 91:1525-1534. [PMID: 37462340 DOI: 10.1002/prot.26546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 10/07/2023]
Abstract
Fatty acid binding proteins (FABPs) are responsible for the long-chain fatty acids (FAs) transport inside the cell. However, despite the years, since their structure is known and the many studies published, there is no definitive answer about the stages of the lipid entry-exit mechanism. Their structure forms a β -barrel of 10 anti-parallel strands with a cap in a helix-turn-helix motif, and there is some consensus on the role of the so-called portal region, involving the second α -helix from the cap ( α 2), β C- β D, and β E- β F turns in FAs exchange. To test the idea of a lid that opens, we performed a soaking experiment on an h-FABP crystal in which the cap is part of the packing contacts, and its movement is strongly restricted. Even in these conditions, we observed the replacement of palmitic acid by 2-Bromohexadecanoic acid (Br-palmitic acid). Our MD simulations reveal a two-step lipid entry process: (i) The travel of the lipid head through the cavity in the order of tens of nanoseconds, and (ii) The accommodation of its hydrophobic tail in hundreds to thousands of nanoseconds. We observed this even in the cases in which the FAs enter the cavity by their tail. During this process, the FAs do not follow a single trajectory, but multiple ones through which they get into the protein cavity. Thanks to the complementary views between experiment and simulation, we can give an approach to a mechanistic view of the exchange process.
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Affiliation(s)
- H Ariel Alvarez
- Instituto de Fisica de Liquidos y Sistemas Biologicos (UNLP-CONICET), Buenos Aires, Argentina
- Departamento de Ciencias Biologicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Buenos Aires, Argentina
- Instituto de Ciencias de la Salud, Universidad Nacional Arturo Jauretche, Buenos Aires, Argentina
| | - Alexandra Cousido-Siah
- Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch-Graffenstaden, France
| | - Yanis R Espinosa
- Instituto de Fisica de Liquidos y Sistemas Biologicos (UNLP-CONICET), Buenos Aires, Argentina
- Departamento de Ciencias del Medio Ambiente, Universidad Francisco de Paula Santander, Facultad de Ciencias Agrarias y del Ambiente, Cúcuta, Colombia
| | - Alberto Podjarny
- Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch-Graffenstaden, France
| | - C Manuel Carlevaro
- Instituto de Fisica de Liquidos y Sistemas Biologicos (UNLP-CONICET), Buenos Aires, Argentina
- Facultad Regional La Plata, Universidad Tecnologica Nacional, Buenos Aires, Argentina
| | - Eduardo Howard
- Instituto de Fisica de Liquidos y Sistemas Biologicos (UNLP-CONICET), Buenos Aires, Argentina
- Facultad Regional Tierra del Fuego, Universidad Tecnologica Nacional, Ushuaia, Tierra del Fuego, Argentina
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3
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Chen H, Guo Y, Ye S, Zhang J, Zhang H, Liu N, Zhou R, Hou T, Xia H, Kang Y, Duan M. On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate. J Chem Inf Model 2023; 63:5232-5243. [PMID: 37574904 DOI: 10.1021/acs.jcim.3c00641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Fatty acids (FAs) are one of the essential energy sources for physiological processes, and they play a vital role in regulating immune and inflammatory responses, promoting cell differentiation and apoptosis, and inhibiting tumor growth. These functions are carried out by FA binding proteins (FABPs) that recognize and transport FAs. Although the crystal structure of the FA-FABPs complex has long been characterized, the mechanism behind FA binding and dissociation from FABP remains unclear. This study employed conventional MD simulations and enhanced sampling technologies to investigate the atomic-scale complexes of heart fatty acid binding proteins and stearic acid (SA). The results revealed two primary pathways for the binding or dissociation of the flexible long-chain ligand, with the orientation of the SA carboxyl head during dissociation determining the chosen path. Conformational changes in the portal region of FABP during the ligand binding/unbinding were found to be trivial, and the overturn of the ″cap″ or the unfolding of the α2 helix was not required. This study resolves the long-standing debate on the binding mechanism of SA with the long-flexible tail to FABP, which significantly improves the understanding of the transport mechanism of FABPs and the development of related therapeutic agents.
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Affiliation(s)
- Haiyi Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
| | - Yue Guo
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Shengqing Ye
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
- Department of Biochemistry & Research Center of Clinical Pharmacy of the First Affiliated Hospital, Zhejiang University School of medicine, Hangzhou 310058, China
| | - Jintu Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
| | - Haotian Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
| | - Na Liu
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Rui Zhou
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Hongguang Xia
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
- Department of Biochemistry & Research Center of Clinical Pharmacy of the First Affiliated Hospital, Zhejiang University School of medicine, Hangzhou 310058, China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Mojie Duan
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
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4
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Abstract
Fatty acid-binding proteins (FABPs) are small lipid-binding proteins abundantly expressed in tissues that are highly active in fatty acid (FA) metabolism. Ten mammalian FABPs have been identified, with tissue-specific expression patterns and highly conserved tertiary structures. FABPs were initially studied as intracellular FA transport proteins. Further investigation has demonstrated their participation in lipid metabolism, both directly and via regulation of gene expression, and in signaling within their cells of expression. There is also evidence that they may be secreted and have functional impact via the circulation. It has also been shown that the FABP ligand binding repertoire extends beyond long-chain FAs and that their functional properties also involve participation in systemic metabolism. This article reviews the present understanding of FABP functions and their apparent roles in disease, particularly metabolic and inflammation-related disorders and cancers.
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Affiliation(s)
- Judith Storch
- Department of Nutritional Sciences and Rutgers Center for Lipid Research, Rutgers University, New Brunswick, New Jersey, United States;
| | - Betina Corsico
- Instituto de Investigaciones Bioquímicas de La Plata, CONICET-UNLP, Facultad de Ciencias Médicas, La Plata, Argentina;
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5
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Bodnariuc I, Lenz S, Renaud-Young M, Butler TM, Ishida H, Vogel HJ, MacCallum JL. A combined computational-biophysical approach to understanding fatty acid binding to FABP7. Biophys J 2023; 122:741-752. [PMID: 36751130 PMCID: PMC10027445 DOI: 10.1016/j.bpj.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 10/21/2022] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Members of the fatty acid binding protein (FABP) family function as intracellular transporters of long-chain fatty acids and other hydrophobic molecules to different cellular compartments. Brain FABP (FABP7) exhibits ligand-directed differences in cellular transport. For example, when FABP7 binds to docosahexaenoic acid (DHA), the complex relocates to the nucleus and influences transcriptional activity, whereas FABP7 bound with monosaturated fatty acids remains in the cytosol. Preferential binding of FABP7 to polyunsaturated fatty acids like DHA has been previously observed and is thought to play a role in differential localization. However, we find that at 37°C, FABP7 does not display strong selectivity, suggesting that the conformational ensemble of FABP7 and its perturbation upon binding may be important. We use molecular dynamics simulations, NMR, and a variety of biophysical techniques to better understand the conformational ensemble of FABP7, how it is perturbed by fatty acid binding, and how this may be related to ligand-directed transport. We find that FABP7 has high degree of conformational heterogeneity that is substantially reduced upon ligand binding. We also observe substantial heterogeneity in ligand binding poses, which is consistent with our finding that ligand binding is resistant to mutations in key polar residues in the binding pocket. Our NMR experiments show that DHA binding leads to chemical shift perturbations in residues near the nuclear localization signal, which may point toward a mechanism of differential transport.
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Affiliation(s)
- Iulia Bodnariuc
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
| | - Stefan Lenz
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
| | | | - Tanille M Butler
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
| | - Hiroaki Ishida
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Hans J Vogel
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Justin L MacCallum
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada.
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6
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Lenz S, Bodnariuc I, Renaud-Young M, Butler TM, MacCallum JL. Understanding FABP7 binding to fatty acid micelles and membranes. Biophys J 2023; 122:603-615. [PMID: 36698315 PMCID: PMC9989940 DOI: 10.1016/j.bpj.2023.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/08/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Fatty acid-binding proteins (FABPs) are chaperones that facilitate the transport of long-chain fatty acids within the cell and can provide cargo-dependent localization to specific cellular compartments. Understanding the nature of this transport is important because lipid signaling functions are associated with metabolic pathways impacting disease pathologies including cancer, autism, and schizophrenia. FABPs often associate with cell membranes to acquire and deliver their bound cargo as part of transport. We focus on brain FABP (FABP7), which demonstrates localization to the cytoplasm and nucleus, influencing transcription and fatty acid metabolism. We use a combined biophysical-computational approach to elucidate the interaction between FABP7 and model membranes. Specifically, we use multiple experiments to demonstrate that FABP7 can bind oleic acid and docosahexaenoic acid micelles. Data from NMR and multiscale molecular dynamics simulations reveal that the interaction with micelles is through FABP7's portal region residues. Simulations suggest that binding to membranes occurs through the same residues as micelles. Simulations also capture binding events where fatty acids dissociate from the membrane and enter FABP7's binding pocket. Overall, our data shed light on the interactions between FABP7 and OA or DHA micelles and provide insight into the transport of long-chain fatty acids.
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Affiliation(s)
- Stefan Lenz
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
| | - Iulia Bodnariuc
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
| | | | - Tanille M Butler
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
| | - Justin L MacCallum
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada.
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7
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Bonsall S, Hubbard S, Jithin U, Anslow J, Todd D, Rowding C, Filarowski T, Duly G, Wilson R, Porter J, Turega S, Haywood-Small S. Water-Soluble Truncated Fatty Acid-Porphyrin Conjugates Provide Photo-Sensitizer Activity for Photodynamic Therapy in Malignant Mesothelioma. Cancers (Basel) 2022; 14:5446. [PMID: 36358864 PMCID: PMC9654571 DOI: 10.3390/cancers14215446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/22/2022] [Accepted: 10/28/2022] [Indexed: 03/07/2024] Open
Abstract
Clinical trials evaluating intrapleural photodynamic therapy (PDT) are ongoing for mesothelioma. Several issues still hinder the development of PDT, such as those related to the inherent properties of photosensitizers. Herein, we report the synthesis, photophysical, and photobiological properties of three porphyrin-based photosensitizers conjugated to truncated fatty acids (C5SHU to C7SHU). Our photosensitizers exhibited excellent water solubility and high PDT efficiency in mesothelioma. As expected, absorption spectroscopy confirmed an increased aggregation as a consequence of extending the fatty acid chain length. In vitro PDT activity was studied using human mesothelioma cell lines (biphasic MSTO-211H cells and epithelioid NCI-H28 cells) alongside a non-malignant mesothelial cell line (MET-5A). The PDT effect of these photosensitizers was initially assessed using the colorimetric WST-8 cell viability assay and the mode of cell death was determined via flow cytometry of Annexin V-FITC/PI-stained cells. Photosensitizers appeared to selectively localize within the non-nuclear compartments of cells before exhibiting high phototoxicity. Both apoptosis and necrosis were induced at 24 and 48 h. As our pentanoic acid-derivatized porphyrin (C5SHU) induced the largest anti-tumor effect in this study, we put this forward as an anti-tumor drug candidate in PDT and photo-imaging diagnosis in mesothelioma.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Sarah Haywood-Small
- Biomolecular Sciences Research Centre, Sheffield Hallam University, City Campus, Howard Street, Sheffield S1 1WB, UK
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8
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Lu Y, Yang GZ, Yang D. Effects of ligand binding on dynamics of fatty acid binding protein and interactions with membranes. Biophys J 2022; 121:4024-4032. [PMID: 36196055 PMCID: PMC9675020 DOI: 10.1016/j.bpj.2022.09.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/19/2022] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
Intracellular transport of fatty acids involves binding of ligands to their carrier fatty acid binding proteins (FABPs) and interactions of ligand-free and -bound FABPs with membranes. Previous studies focused on ligand-free FABPs. Here, our amide hydrogen exchange data showed that oleic acid binding to human intestinal FABP (hIFABP) stabilizes the protein, most likely through enhancing the hydrogen-bonding network, and induces rearrangement of sidechains even far away from the ligand binding site. Using NMR relaxation techniques, we found that the ligand binding affects not only conformational exchanges between major and minor states but also the affinity of hIFABP to nanodiscs. Analyses of the relaxation and amide exchange data suggested that two minor native-like states existing in both ligand-free and -bound hIFABPs originate from global "breathing" motions, while one minor native-like state comes from local motions. The amide hydrogen exchange data also indicated that helix αII undergoes local unfolding through which ligands can exit from the binding cavity.
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Affiliation(s)
- Yimei Lu
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Gabriel Zhang Yang
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, Singapore.
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9
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Huang X, Zhou Y, Sun Y, Wang Q. Intestinal fatty acid binding protein: A rising therapeutic target in lipid metabolism. Prog Lipid Res 2022; 87:101178. [PMID: 35780915 DOI: 10.1016/j.plipres.2022.101178] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 10/17/2022]
Abstract
Fatty acid binding proteins (FABPs) are key proteins in lipid transport, and the isoforms are segregated according to their tissue origins. Several isoforms, such as adipose-FABP and epidermal-FABP, have been shown to participate in multiple pathologic processes due to their ubiquitous expression. Intestinal fatty acid binding protein, also termed FABP2 or I-FABP, is specifically expressed in the small intestine. FABP2 can traffic lipids from the intestinal lumen to enterocytes and bind superfluous fatty acids to maintain a steady pool of fatty acids in the epithelium. As a lipid chaperone, FABP2 can also carry lipophilic drugs to facilitate targeted transport. When the integrity of the intestinal epithelium is disrupted, FABP2 is released into the circulation. Thus, it can potentially serve as a clinical biomarker. In this review, we discuss the pivotal role of FABP2 in intestinal lipid metabolism. We also summarize the molecular interactions that have been reported to date, highlighting the clinical prospects of FABP2 research.
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Affiliation(s)
- Xi Huang
- Shanghai Institute of Immunology, Department of Gastroenterology of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Youci Zhou
- Shanghai Institute of Immunology, Department of Gastroenterology of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yunwei Sun
- Shanghai Institute of Immunology, Department of Gastroenterology of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qijun Wang
- Shanghai Institute of Immunology, Department of Gastroenterology of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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10
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Gullett JM, Cuypers MG, Grace CR, Pant S, Subramanian C, Tajkhorshid E, Rock CO, White SW. Identification of Structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes. J Biol Chem 2022; 298:101676. [PMID: 35122790 PMCID: PMC8892158 DOI: 10.1016/j.jbc.2022.101676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 12/31/2022] Open
Abstract
Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein–FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a “closed” FakB1 state to an “open” state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic α-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.
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Affiliation(s)
- Jessica M Gullett
- Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Maxime G Cuypers
- Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christy R Grace
- Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shashank Pant
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chitra Subramanian
- Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Charles O Rock
- Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Stephen W White
- Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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11
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Lu Y, Yang D. Conformational exchange of fatty acid binding protein induced by protein-nanodisc interactions. Biophys J 2021; 120:4672-4681. [PMID: 34600898 DOI: 10.1016/j.bpj.2021.09.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/20/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022] Open
Abstract
Fatty acid binding proteins (FABPs) can facilitate the transfer of long-chain fatty acids between intracellular membranes across considerable distances. The transfer process involves fatty acids, their donor membrane and acceptor membrane, and FABPs, implying that potential protein-membrane interactions exist. Despite intensive studies on FABP-membrane interactions, the interaction mode remains elusive, and the protein-membrane association and dissociation rates are inconsistent. In this study, we used nanodiscs (NDs) as mimetic membranes to investigate FABP-membrane interactions. Our NMR experiments showed that human intestinal FABP interacts weakly with both negatively charged and neutral membranes, but it prefers the negatively charged one. Through simultaneous analysis of NMR relaxation in the rotating-frame (R1ρ), relaxation dispersion, chemical exchange saturation transfer, and dark-state exchange saturation transfer data, we estimated the affinity of the protein to negatively charged NDs, the dissociation rate, and apparent association rate. We further showed that the protein in the ND-bound state adopts a conformation different from the native structure and the second helix is very likely involved in interactions with NDs. We also found a membrane-induced FABP conformational state that exists only in the presence of NDs. This state is native-like, different from other conformational states in structure, unbound to NDs, and in dynamic equilibrium with the ND-bound state.
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Affiliation(s)
- Yimei Lu
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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12
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Zhou Y, van Zijl PCM, Xu J, Yadav NN. Mechanism and quantitative assessment of saturation transfer for water-based detection of the aliphatic protons in carbohydrate polymers. Magn Reson Med 2020; 85:1643-1654. [PMID: 32970889 DOI: 10.1002/mrm.28503] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/20/2020] [Accepted: 08/10/2020] [Indexed: 12/23/2022]
Abstract
PURPOSE CEST MRI experiments of mobile macromolecules, for example, proteins, carbohydrates, and phospholipids, often show signals due to saturation transfer from aliphatic protons to water. Currently, the mechanism of this nuclear Overhauser effect (NOE)-based transfer pathway is not completely understood and could be due either to NOEs directly to bound water or NOEs relayed intramolecularly via exchangeable protons. We used glycogen as a model system to investigate this saturation transfer pathway in sugar polymer solution. METHODS To determine whether proton exchange affected saturation transfer, saturation spectra (Z-spectra) were measured for glycogen solutions of different pH, D2 O/H2 O ratio, and glycogen particle size. A theoretical model was derived to analytically describe the NOE-based signals in these spectra. Numerical simulations were performed to verify this theory, which was further tested by fitting experimental data for different exchange regimes. RESULTS Signal intensities of aliphatic NOEs in Z-spectra of glycogen in D2 O solution were influenced by hydroxyl proton exchange rates, whereas those in H2 O were not. This indicates that the primary transfer pathway is an exchange-relayed NOE from these aliphatic protons to neighboring hydroxyl protons, followed by the exchange to water protons. Experimental data for glycogen solutions in D2 O and H2 O could be analyzed successfully using an analytical theory derived for such relayed NOE transfer, which was further validated using numerical simulations with the Bloch equations. CONCLUSION The predominant mechanism underlying aliphatic signals in Z-spectra of mobile carbohydrate polymers is intramolecular relayed NOE transfer followed by proton exchange.
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Affiliation(s)
- Yang Zhou
- The Russell H. Morgan Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Peter C M van Zijl
- The Russell H. Morgan Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Jiadi Xu
- The Russell H. Morgan Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Nirbhay N Yadav
- The Russell H. Morgan Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
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13
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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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14
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Xiao T, Lu Y, Fan JS, Yang D. Ligand Entry into Fatty Acid Binding Protein via Local Unfolding Instead of Gap Widening. Biophys J 2020; 118:396-402. [PMID: 31870540 DOI: 10.1016/j.bpj.2019.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/25/2019] [Accepted: 12/03/2019] [Indexed: 11/24/2022] Open
Abstract
Fatty acid binding proteins play an important role in the transportation of fatty acids. Despite intensive studies, how fatty acids enter the protein cavity for binding is still controversial. Here, a gap-closed variant of human intestinal fatty acid binding protein was generated by mutagenesis, in which the gap is locked by a disulfide bridge. According to its structure determined here by NMR, this variant has no obvious openings as the ligand entrance and the gap cannot be widened by internal dynamics. Nevertheless, it still takes up fatty acids and other ligands. NMR relaxation dispersion, chemical exchange saturation transfer, and hydrogen-deuterium exchange experiments show that the variant exists in a major native state, two minor native-like states, and two locally unfolded states in aqueous solution. Local unfolding of either βB-βD or helix 2 can generate an opening large enough for ligands to enter the protein cavity, but only the fast local unfolding of helix 2 is relevant to the ligand entry process.
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Affiliation(s)
- Tianshu Xiao
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Yimei Lu
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Jing-Song Fan
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, Singapore.
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15
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The ligand-mediated affinity of brain-type fatty acid-binding protein for membranes determines the directionality of lipophilic cargo transport. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:158506. [DOI: 10.1016/j.bbalip.2019.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 07/29/2019] [Accepted: 08/08/2019] [Indexed: 01/22/2023]
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16
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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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17
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The Observation of Ligand-Binding-Relevant Open States of Fatty Acid Binding Protein by Molecular Dynamics Simulations and a Markov State Model. Int J Mol Sci 2019; 20:ijms20143476. [PMID: 31311155 PMCID: PMC6678811 DOI: 10.3390/ijms20143476] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/04/2019] [Accepted: 07/10/2019] [Indexed: 12/21/2022] Open
Abstract
As a member of the fatty acids transporter family, the heart fatty acid binding proteins (HFABPs) are responsible for many important biological activities. The binding mechanism of fatty acid with FABP is critical to the understanding of FABP functions. The uncovering of binding-relevant intermediate states and interactions would greatly increase our knowledge of the binding process. In this work, all-atom molecular dynamics (MD) simulations were performed to characterize the structural properties of nativelike intermediate states. Based on multiple 6 μs MD simulations and Markov state model (MSM) analysis, several "open" intermediate states were observed. The transition rates between these states and the native closed state are in good agreement with the experimental measurements, which indicates that these intermediate states are binding relevant. As a common property in the open states, the partially unfolded α2 helix generates a larger portal and provides the driving force to facilitate ligand binding. On the other side, there are two kinds of open states for the ligand-binding HFABP: one has the partially unfolded α2 helix, and the other has the looser β-barrel with disjointing βD-βE strands. Our results provide atomic-level descriptions of the binding-relevant intermediate states and could improve our understanding of the binding mechanism.
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18
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Matsudaira PT, Verma CS. Editorial. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 143:1-4. [PMID: 30951764 DOI: 10.1016/j.pbiomolbio.2019.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paul T Matsudaira
- Department of Biological Science, National University of Singapore, 14 Science Drive 4, 117543, Singapore; Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore; MechanoBiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore.
| | - Chandra S Verma
- Department of Biological Science, National University of Singapore, 14 Science Drive 4, 117543, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr, 637551, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, 138671, Singapore.
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19
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Chatterjee SD, Ubbink M, van Ingen H. Removal of slow-pulsing artifacts in in-phase 15N relaxation dispersion experiments using broadband 1H decoupling. JOURNAL OF BIOMOLECULAR NMR 2018; 71:69-77. [PMID: 29860650 PMCID: PMC6061081 DOI: 10.1007/s10858-018-0193-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
Understanding of the molecular mechanisms of protein function requires detailed insight into the conformational landscape accessible to the protein. Conformational changes can be crucial for biological processes, such as ligand binding, protein folding, and catalysis. NMR spectroscopy is exquisitely sensitive to such dynamic changes in protein conformations. In particular, Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments are a powerful tool to investigate protein dynamics on a millisecond time scale. CPMG experiments that probe the chemical shift modulation of 15N in-phase magnetization are particularly attractive, due to their high sensitivity. These experiments require high power 1H decoupling during the CPMG period to keep the 15N magnetization in-phase. Recently, an improved version of the in-phase 15N-CPMG experiment was introduced, offering greater ease of use by employing a single 1H decoupling power for all CPMG pulsing rates. In these experiments however, incomplete decoupling of off-resonance amide 1H spins introduces an artefactual dispersion of relaxation rates, the so-called slow-pulsing artifact. Here, we analyze the slow-pulsing artifact in detail and demonstrate that it can be suppressed through the use of composite pulse decoupling (CPD). We report the performances of various CPD schemes and show that CPD decoupling based on the 90x-240y-90x element results in high-quality dispersion curves free of artifacts, even for amides with high 1H offset.
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Affiliation(s)
- Soumya Deep Chatterjee
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O Box 9502, 2300 RA, Leiden, The Netherlands
| | - Marcellus Ubbink
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O Box 9502, 2300 RA, Leiden, The Netherlands
| | - Hugo van Ingen
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O Box 9502, 2300 RA, Leiden, The Netherlands.
- NMR Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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20
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Equilibrium folding dynamics of meACP in water, heavy water, and low concentration of urea. Sci Rep 2017; 7:16156. [PMID: 29170533 PMCID: PMC5700953 DOI: 10.1038/s41598-017-16449-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/13/2017] [Indexed: 12/21/2022] Open
Abstract
Many proteins fold in apparent two-state behavior, as partially folded intermediates only transiently accumulate and easily escape detection. Besides a native form and a mainly unfolded form, we captured a partially unfolded form of an acyl carrier protein from Micromonospora echinospora (meACP) in the folding/unfolding equilibrium using chemical exchange saturation transfer NMR experiments. The C-terminal region of the partially unfolded form is mainly folded and the N-terminal is unfolded. Furthermore, to understand how the folding process of meACP is influenced by solvent environments, we compared the folding dynamics of meACP in D2O, H2O and low concentration of urea. As the environment becomes more denaturing from D2O to H2O and then to urea, the unfolded state becomes increasingly populated, and the folding rate decreases. Adding a small amount of urea, which does not change solvent viscosity, has little effects on the unfolding rates, while changing H2O to D2O reduces the unfolding rates possibly due to the increase of solvent viscosity. The quantified solvent effects on the protein folding Gibbs energy and activation energy suggest that the transition state of folding may have a similar structure to the native state of the protein.
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21
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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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22
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Coexistence of multiple minor states of fatty acid binding protein and their functional relevance. Sci Rep 2016; 6:34171. [PMID: 27677899 PMCID: PMC5039767 DOI: 10.1038/srep34171] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/07/2016] [Indexed: 01/01/2023] Open
Abstract
Proteins are dynamic over a wide range of timescales, but determining the number of distinct dynamic processes and identifying functionally relevant dynamics are still challenging. Here we present the study on human intestinal fatty acid binding protein (hIFABP) using a novel analysis of 15N relaxation dispersion (RD) and chemical shift saturation transfer (CEST) experiments. Through combined analysis of the two types of experiments, we found that hIFABP exists in a four-state equilibrium in which three minor states interconvert directly with the major state. According to conversion rates from the major “closed” state to minor states, these minor states are irrelevant to the function of fatty acid transport. Based on chemical shifts of the minor states which could not be determined from RD data alone but were extracted from a combined analysis of RD and CEST data, we found that all the minor states are native-like. This conclusion is further supported by hydrogen-deuterium exchange experiments. Direct conversions between the native state and native-like intermediate states may suggest parallel multitrack unfolding/folding pathways of hIFABP. Moreover, hydrogen-deuterium exchange data indicate the existence of another locally unfolded minor state that is relevant to the fatty acid entry process.
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