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Krokengen OC, Touma C, Mularski A, Sutinen A, Dunkel R, Ytterdal M, Raasakka A, Mertens HDT, Simonsen AC, Kursula P. The cytoplasmic tail of myelin protein zero induces morphological changes in lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184368. [PMID: 38971517 DOI: 10.1016/j.bbamem.2024.184368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
The major myelin protein expressed by the peripheral nervous system Schwann cells is protein zero (P0), which represents 50% of the total protein content in myelin. This 30-kDa integral membrane protein consists of an immunoglobulin (Ig)-like domain, a transmembrane helix, and a 69-residue C-terminal cytoplasmic tail (P0ct). The basic residues in P0ct contribute to the tight packing of myelin lipid bilayers, and alterations in the tail affect how P0 functions as an adhesion molecule necessary for the stability of compact myelin. Several neurodegenerative neuropathies are related to P0, including the more common Charcot-Marie-Tooth disease (CMT) and Dejerine-Sottas syndrome (DSS) as well as rare cases of motor and sensory polyneuropathy. We found that high P0ct concentrations affected the membrane properties of bicelles and induced a lamellar-to-inverted hexagonal phase transition, which caused bicelles to fuse into long, protein-containing filament-like structures. These structures likely reflect the formation of semicrystalline lipid domains with potential relevance for myelination. Not only is P0ct important for stacking lipid membranes, but time-lapse fluorescence microscopy also shows that it might affect membrane properties during myelination. We further describe recombinant production and low-resolution structural characterization of full-length human P0. Our findings shed light on P0ct effects on membrane properties, and with the successful purification of full-length P0, we have new tools to study the role of P0 in myelin formation and maintenance in vitro.
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Affiliation(s)
- Oda C Krokengen
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Christine Touma
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anna Mularski
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Aleksi Sutinen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ryan Dunkel
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Marie Ytterdal
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY, Hamburg, Germany
| | - Adam Cohen Simonsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway; Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
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2
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Samal RR, Subudhi U. Biochemical and biophysical interaction of rare earth elements with biomacromolecules: A comprehensive review. CHEMOSPHERE 2024; 357:142090. [PMID: 38648983 DOI: 10.1016/j.chemosphere.2024.142090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/06/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
The growing utilization of rare earth elements (REEs) in industrial and technological applications has captured global interest, leading to the development of high-performance technologies in medical diagnosis, agriculture, and other electronic industries. This accelerated utilization has also raised human exposure levels, resulting in both favourable and unfavourable impacts. However, the effects of REEs are dependent on their concentration and molecular species. Therefore, scientific interest has increased in investigating the molecular interactions of REEs with biomolecules. In this current review, particular attention was paid to the molecular mechanism of interactions of Lanthanum (La), Cerium (Ce), and Gadolinium (Gd) with biomolecules, and the biological consequences were broadly interpreted. The review involved gathering and evaluating a vast scientific collection which primarily focused on the impact associated with REEs, ranging from earlier reports to recent discoveries, including studies in human and animal models. Thus, understanding the molecular interactions of each element with biomolecules will be highly beneficial in elucidating the consequences of REEs accumulation in the living organisms.
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Affiliation(s)
- Rashmi R Samal
- Biochemistry & Biophysics Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals and Materials Technology, Bhubaneswar, 751013, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Umakanta Subudhi
- Biochemistry & Biophysics Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals and Materials Technology, Bhubaneswar, 751013, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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3
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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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4
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Agellon LB. Importance of fatty acid binding proteins in cellular function and organismal metabolism. J Cell Mol Med 2023; 28:e17703. [PMID: 36876733 PMCID: PMC10902576 DOI: 10.1111/jcmm.17703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/25/2023] [Accepted: 02/14/2023] [Indexed: 03/07/2023] Open
Abstract
Fatty acid binding proteins (Fabps) are small soluble proteins that are abundant in the cytosol. These proteins are known to bind a myriad of small hydrophobic molecules and have been postulated to serve a variety of roles, yet their precise functions have remained an enigma over half a century of study. Here, we consider recent findings, along with the cumulative findings contributed by many laboratories working on Fabps over the last half century, to synthesize a new outlook for what functions Fabps serve in cells and organisms. Collectively, the findings illustrate that Fabps function as versatile multi-purpose devices serving as sensors, conveyors and modulators to enable cells to detect and handle a specific class of metabolites, and to adjust their metabolic capacity and efficiency.
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Affiliation(s)
- Luis B Agellon
- School of Human Nutrition, McGill University, Ste. Anne de Bellevue, Quebec, Canada
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5
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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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6
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Lipids in Pathophysiology and Development of the Membrane Lipid Therapy: New Bioactive Lipids. MEMBRANES 2021; 11:membranes11120919. [PMID: 34940418 PMCID: PMC8708953 DOI: 10.3390/membranes11120919] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/19/2022]
Abstract
Membranes are mainly composed of a lipid bilayer and proteins, constituting a checkpoint for the entry and passage of signals and other molecules. Their composition can be modulated by diet, pathophysiological processes, and nutritional/pharmaceutical interventions. In addition to their use as an energy source, lipids have important structural and functional roles, e.g., fatty acyl moieties in phospholipids have distinct impacts on human health depending on their saturation, carbon length, and isometry. These and other membrane lipids have quite specific effects on the lipid bilayer structure, which regulates the interaction with signaling proteins. Alterations to lipids have been associated with important diseases, and, consequently, normalization of these alterations or regulatory interventions that control membrane lipid composition have therapeutic potential. This approach, termed membrane lipid therapy or membrane lipid replacement, has emerged as a novel technology platform for nutraceutical interventions and drug discovery. Several clinical trials and therapeutic products have validated this technology based on the understanding of membrane structure and function. The present review analyzes the molecular basis of this innovative approach, describing how membrane lipid composition and structure affects protein-lipid interactions, cell signaling, disease, and therapy (e.g., fatigue and cardiovascular, neurodegenerative, tumor, infectious diseases).
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7
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Brysbaert G, Lensink MF. Centrality Measures in Residue Interaction Networks to Highlight Amino Acids in Protein–Protein Binding. FRONTIERS IN BIOINFORMATICS 2021; 1:684970. [PMID: 36303777 PMCID: PMC9581030 DOI: 10.3389/fbinf.2021.684970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/17/2021] [Indexed: 12/21/2022] Open
Abstract
Residue interaction networks (RINs) describe a protein structure as a network of interacting residues. Central nodes in these networks, identified by centrality analyses, highlight those residues that play a role in the structure and function of the protein. However, little is known about the capability of such analyses to identify residues involved in the formation of macromolecular complexes. Here, we performed six different centrality measures on the RINs generated from the complexes of the SKEMPI 2 database of changes in protein–protein binding upon mutation in order to evaluate the capability of each of these measures to identify major binding residues. The analyses were performed with and without the crystallographic water molecules, in addition to the protein residues. We also investigated the use of a weight factor based on the inter-residue distances to improve the detection of these residues. We show that for the identification of major binding residues, closeness, degree, and PageRank result in good precision, whereas betweenness, eigenvector, and residue centrality analyses give a higher sensitivity. Including water in the analysis improves the sensitivity of all measures without losing precision. Applying weights only slightly raises the sensitivity of eigenvector centrality analysis. We finally show that a combination of multiple centrality analyses is the optimal approach to identify residues that play a role in protein–protein interaction.
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8
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Uusitalo M, Klenow MB, Laulumaa S, Blakeley MP, Simonsen AC, Ruskamo S, Kursula P. Human myelin protein P2: from crystallography to time-lapse membrane imaging and neuropathy-associated variants. FEBS J 2021; 288:6716-6735. [PMID: 34138518 DOI: 10.1111/febs.16079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 12/11/2022]
Abstract
Peripheral myelin protein 2 (P2) is a fatty acid-binding protein expressed in vertebrate peripheral nervous system myelin, as well as in human astrocytes. Suggested functions of P2 include membrane stacking and lipid transport. Mutations in the PMP2 gene, encoding P2, are associated with Charcot-Marie-Tooth disease (CMT). Recent studies have revealed three novel PMP2 mutations in CMT patients. To shed light on the structure and function of these P2 variants, we used X-ray and neutron crystallography, small-angle X-ray scattering, circular dichroism spectroscopy, computer simulations and lipid binding assays. The crystal and solution structures of the I50del, M114T and V115A variants of P2 showed minor differences to the wild-type protein, whereas their thermal stability was reduced. Vesicle aggregation assays revealed no change in membrane stacking characteristics, while the variants showed altered fatty acid binding. Time-lapse imaging of lipid bilayers indicated formation of double-membrane structures induced by P2, which could be related to its function in stacking of two myelin membrane surfaces in vivo. In order to better understand the links between structure, dynamics and function, the crystal structure of perdeuterated P2 was refined from room temperature data using neutrons and X-rays, and the results were compared to simulations and cryocooled crystal structures. Our data indicate similar properties for all known human P2 CMT variants; while crystal structures are nearly identical, thermal stability and function of CMT variants are impaired. Our data provide new insights into the structure-function relationships and dynamics of P2 in health and disease.
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Affiliation(s)
- Maiju Uusitalo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Martin Berg Klenow
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.,European Spallation Source, Lund, Sweden
| | | | - Adam Cohen Simonsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.,Department of Biomedicine, University of Bergen, Norway
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9
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Ruskamo S, Krokengen OC, Kowal J, Nieminen T, Lehtimäki M, Raasakka A, Dandey VP, Vattulainen I, Stahlberg H, Kursula P. Cryo-EM, X-ray diffraction, and atomistic simulations reveal determinants for the formation of a supramolecular myelin-like proteolipid lattice. J Biol Chem 2020; 295:8692-8705. [PMID: 32265298 DOI: 10.1074/jbc.ra120.013087] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/31/2020] [Indexed: 12/15/2022] Open
Abstract
Myelin protein P2 is a peripheral membrane protein of the fatty acid-binding protein family that functions in the formation and maintenance of the peripheral nerve myelin sheath. Several P2 gene mutations cause human Charcot-Marie-Tooth neuropathy, but the mature myelin sheath assembly mechanism is unclear. Here, cryo-EM of myelin-like proteolipid multilayers revealed an ordered three-dimensional (3D) lattice of P2 molecules between stacked lipid bilayers, visualizing supramolecular assembly at the myelin major dense line. The data disclosed that a single P2 layer is inserted between two bilayers in a tight intermembrane space of ∼3 nm, implying direct interactions between P2 and two membrane surfaces. X-ray diffraction from P2-stacked bicelle multilayers revealed lateral protein organization, and surface mutagenesis of P2 coupled with structure-function experiments revealed a role for both the portal region of P2 and its opposite face in membrane interactions. Atomistic molecular dynamics simulations of P2 on model membrane surfaces suggested that Arg-88 is critical for P2-membrane interactions, in addition to the helical lid domain. Negatively charged lipid headgroups stably anchored P2 on the myelin-like bilayer surface. Membrane binding may be accompanied by opening of the P2 β-barrel structure and ligand exchange with the apposing bilayer. Our results provide an unprecedented view into an ordered, multilayered biomolecular membrane system induced by the presence of a peripheral membrane protein from human myelin. This is an important step toward deciphering the 3D assembly of a mature myelin sheath at the molecular level.
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Affiliation(s)
- Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
| | - Oda C Krokengen
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | - Julia Kowal
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, 4058 Basel, Switzerland
| | - Tuomo Nieminen
- Computational Physics Laboratory, Tampere University, 33014 Tampere, Finland
| | - Mari Lehtimäki
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | - Venkata P Dandey
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, 4058 Basel, Switzerland
| | - Ilpo Vattulainen
- Computational Physics Laboratory, Tampere University, 33014 Tampere, Finland; Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, 4058 Basel, Switzerland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; Biocenter Oulu, University of Oulu, 90014 Oulu, Finland; Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
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10
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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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11
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Xu H, Diolintzi A, Storch J. Fatty acid-binding proteins: functional understanding and diagnostic implications. Curr Opin Clin Nutr Metab Care 2019; 22:407-412. [PMID: 31503024 PMCID: PMC9940447 DOI: 10.1097/mco.0000000000000600] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Fatty acid-binding proteins (FABPs) are a family of small, abundant proteins with highly tissue-specific expression patterns whose different functions remain incompletely understood. The purpose of this review is to summarize recent findings regarding FABP functions and mechanisms of action, including their potential utilization as serum markers of tissue-specific metabolic diseases. RECENT FINDINGS FABPs are important not only in their tissues of origin but also appear to influence the metabolism and function of tissues distal to their sites of expression. This may be secondary to metabolic changes in their primary tissues, and/or a result of FABP secretion from these tissues leading to effects on distal sites. Their levels in the circulation are increasingly explored as potential biomarkers for tissue-specific disease prognosis and progression. SUMMARY The nine fatty acid-binding members of the FABP family have unique tissue-specific functions and important secondary effects on tissues in which they are not expressed. For many of the FABPs, circulating levels may be indicative of disease processes related to their primary tissues, and may influence physiological function in distal tissues.
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Affiliation(s)
- Heli Xu
- Department of Nutritional Sciences, Rutgers University, New Brunswick,
- Rutgers Center for Lipid Research, New Jersey, USA
| | - Anastasia Diolintzi
- Department of Kinesiology and Health, New Jersey, USA
- Rutgers Center for Lipid Research, New Jersey, USA
| | - Judith Storch
- Department of Nutritional Sciences, Rutgers University, New Brunswick,
- Rutgers Center for Lipid Research, New Jersey, USA
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12
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Laulumaa S, Koza MM, Seydel T, Kursula P, Natali F. A Quasielastic Neutron Scattering Investigation on the Molecular Self-Dynamics of Human Myelin Protein P2. J Phys Chem B 2019; 123:8178-8185. [PMID: 31483648 DOI: 10.1021/acs.jpcb.9b05320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The human myelin protein P2 is a membrane binding protein believed to maintain correct lipid composition and organization in peripheral nerve myelin. Its function is related to its ability to stack membranes, and this function can be enhanced by the P38G mutation, whereby the overall protein structure does not change but the molecular dynamics increase. Mutations in P2 are linked to human peripheral neuropathy. Here, the dynamics of wild-type P2 and the P38G variant were studied using quasielastic neutron scattering on time scales from 10 ps to 1 ns at 300 K. The results suggest that the mutant protein dynamics are increased on both the fastest and the slowest measured time scales, by increasing the dynamics amplitude and/or the portion of atoms participating in the movement.
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Affiliation(s)
- Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu , University of Oulu , Oulu , Finland.,European Spallation Source , Lund , Sweden
| | | | | | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu , University of Oulu , Oulu , Finland.,Department of Biomedicine , University of Bergen , Bergen , Norway
| | - Francesca Natali
- Institut Laue-Langevin , Grenoble , France.,CNR-IOM, OGG , Grenoble , France
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13
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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: 9] [Impact Index Per Article: 1.8] [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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Laulumaa S, Kursula P. Sub-Atomic Resolution Crystal Structures Reveal Conserved Geometric Outliers at Functional Sites. Molecules 2019; 24:molecules24173044. [PMID: 31443388 PMCID: PMC6749445 DOI: 10.3390/molecules24173044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 01/28/2023] Open
Abstract
Myelin protein 2 (P2) is a peripheral membrane protein of the vertebrate nervous system myelin sheath, having possible roles in both lipid transport and 3D molecular organization of the multilayered myelin membrane. We extended our earlier crystallographic studies on human P2 and refined its crystal structure at an ultrahigh resolution of 0.72 Å in perdeuterated form and 0.86 Å in hydrogenated form. Characteristic differences in C–H…O hydrogen bond patterns were observed between extended β strands, kinked or ending strands, and helices. Often, side-chain C–H groups engage in hydrogen bonding with backbone carbonyl moieties. The data highlight several amino acid residues with unconventional conformations, including both bent aromatic rings and twisted guanidinium groups on arginine side chains, as well as non-planar peptide bonds. In two locations, such non-ideal conformations cluster, providing proof of local functional strain. Other ultrahigh-resolution protein structures similarly contain chemical groups, which break planarity rules. For example, in Src homology 3 (SH3) domains, a conserved bent aromatic residue is observed near the ligand binding site. Fatty acid binding protein (FABP) 3, belonging to the same family as P2, has several side chains and peptide bonds bent exactly as those in P2. We provide a high-resolution snapshot on non-ideal conformations of amino acid residues under local strain, possibly relevant to biological function. Geometric outliers observed in ultrahigh-resolution protein structures are real and likely relevant for ligand binding and conformational changes. Furthermore, the deuteration of protein and/or solvent are promising variables in protein crystal optimization.
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Affiliation(s)
- Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
- European Spallation Source, 22100 Lund, Sweden
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90014 Oulu, Finland.
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
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Brysbaert G, Mauri T, de Ruyck J, Lensink MF. Identification of Key Residues in Proteins Through Centrality Analysis and Flexibility Prediction with RINspector. ACTA ACUST UNITED AC 2018; 65:e66. [PMID: 30489695 DOI: 10.1002/cpbi.66] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein structures inherently contain information that can be used to decipher their functions, but the exploitation of this knowledge is not trivial. We recently developed an app for the Cytoscape network visualization and analysis program, called RINspector, the goal of which is to integrate two different approaches that identify key residues in a protein structure or complex. The first approach consists of calculating centralities on a residue interaction network (RIN) generated from the three-dimensional structure; the second consists of predicting backbone flexibility and needs only the primary sequence. The identified residues are highly correlated with functional relevance and constitute a good set of targets for mutagenesis experiments. Here we present a protocol that details in a step-by-step fashion how to create a RIN from a structure and then calculate centralities and predict flexibilities. We also discuss how to understand and use the results of the analyses. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Guillaume Brysbaert
- University of Lille, CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, F-59000 Lille, France
| | - Théo Mauri
- University of Lille, CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, F-59000 Lille, France
| | - Jérôme de Ruyck
- University of Lille, CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, F-59000 Lille, France
| | - Marc F Lensink
- University of Lille, CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, F-59000 Lille, France
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