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Verma S, Dangi RS, Rajak MK, Pal RK, Sundd M. The apo-acyl coenzyme A binding protein of Leishmania major forms a unique 'AXXA' motif mediated dimer. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141016. [PMID: 38615987 DOI: 10.1016/j.bbapap.2024.141016] [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: 01/24/2024] [Revised: 03/22/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
Acyl-Coenzyme A binding domain containing proteins (ACBDs) are ubiquitous in nearly all eukaryotes. They can exist as a free protein, or a domain of a large, multidomain, multifunctional protein. Besides modularity, ACBDs also display multiplicity. The same organism may have multiple ACBDs, differing in sequence and organization. By virtue of this diversity, ACBDs perform functions ranging from transport, synthesis, trafficking, signal transduction, transcription, and gene regulation. In plants and some microorganisms, these ACBDs are designated ACBPs (acyl-CoA binding proteins). The simplest ACBD/ACBP is a small, ∼10 kDa, soluble protein, comprising the acyl-CoA binding (ACB) domain. Most of these small ACBDs exist as monomers, while a few show a tendency to oligomerize. In sync with those studies, we report the crystal structure of two ACBDs from Leishmania major, named ACBP103, and ACBP96 based on the number of residues present. Interestingly, ACBP103 crystallized as a monomer and a dimer under different crystallization conditions. Careful examination of the dimer disclosed an exposed 'AXXA' motif in the helix I of the two ACBP103 monomers, aligned in a head-to-tail arrangement in the dimer. Glutaraldehyde cross-linking studies confirm that apo-ACBP103 can self-associate in solution. Isothermal titration calorimetry studies further show that ACBP103 can bind ligands ranging from C8 - to C20-CoA, and the data could be best fit to a 'two sets of sites'/sequential binding site model. Taken together, our studies show that Leishmania major ACBP103 can self-associate in the apo-form through a unique dimerization motif, an interaction that may play an important role in its function.
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Affiliation(s)
- Shalini Verma
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Rohit Singh Dangi
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Manoj Kumar Rajak
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Ravi Kant Pal
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Monica Sundd
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India.
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2
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Dani R, Pawloski W, Chaurasiya DK, Srilatha NS, Agarwal S, Fushman D, Naganathan AN. Conformational Tuning Shapes the Balance between Functional Promiscuity and Specialization in Paralogous Plasmodium Acyl-CoA Binding Proteins. Biochemistry 2023; 62:2982-2996. [PMID: 37788430 PMCID: PMC10774088 DOI: 10.1021/acs.biochem.3c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Paralogous proteins confer enhanced fitness to organisms via complex sequence-conformation codes that shape functional divergence, specialization, or promiscuity. Here, we dissect the underlying mechanism of promiscuous binding versus partial subfunctionalization in paralogues by studying structurally identical acyl-CoA binding proteins (ACBPs) from Plasmodium falciparum that serve as promising drug targets due to their high expression during the protozoan proliferative phase. Combining spectroscopic measurements, solution NMR, SPR, and simulations on two of the paralogues, A16 and A749, we show that minor sequence differences shape nearly every local and global conformational feature. A749 displays a broader and heterogeneous native ensemble, weaker thermodynamic coupling and cooperativity, enhanced fluctuations, and a larger binding pocket volume compared to A16. Site-specific tryptophan probes signal a graded reduction in the sampling of substates in the holo form, which is particularly apparent in A749. The paralogues exhibit a spectrum of binding affinities to different acyl-CoAs with A749, the more promiscuous and hence the likely ancestor, binding 1000-fold stronger to lauroyl-CoA under physiological conditions. We thus demonstrate how minor sequence changes modulate the extent of long-range interactions and dynamics, effectively contributing to the molecular evolution of contrasting functional repertoires in paralogues.
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Affiliation(s)
- Rahul Dani
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Westley Pawloski
- Center for Biomolecular Structure & Organization, Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Dhruv Kumar Chaurasiya
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Sonal Agarwal
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - David Fushman
- Center for Biomolecular Structure & Organization, Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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3
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Melnikova DN, Finkina EI, Bogdanov IV, Tagaev AA, Ovchinnikova TV. Features and Possible Applications of Plant Lipid-Binding and Transfer Proteins. MEMBRANES 2022; 13:2. [PMID: 36676809 PMCID: PMC9866449 DOI: 10.3390/membranes13010002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
In plants, lipid trafficking within and inside the cell is carried out by lipid-binding and transfer proteins. Ligands for these proteins are building and signaling lipid molecules, secondary metabolites with different biological activities due to which they perform diverse functions in plants. Many different classes of such lipid-binding and transfer proteins have been found, but the most common and represented in plants are lipid transfer proteins (LTPs), pathogenesis-related class 10 (PR-10) proteins, acyl-CoA-binding proteins (ACBPs), and puroindolines (PINs). A low degree of amino acid sequence homology but similar spatial structures containing an internal hydrophobic cavity are common features of these classes of proteins. In this review, we summarize the latest known data on the features of these protein classes with particular focus on their ability to bind and transfer lipid ligands. We analyzed the structural features of these proteins, the diversity of their possible ligands, the key amino acids participating in ligand binding, the currently known mechanisms of ligand binding and transferring, as well as prospects for possible application.
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Affiliation(s)
- Daria N. Melnikova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| | - Ekaterina I. Finkina
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Ivan V. Bogdanov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Andrey A. Tagaev
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
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4
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Udupa P, Kumar A, Parit R, Ghosh DK. Acyl-CoA binding protein regulates nutrient-dependent autophagy. Metabolism 2022:155338. [PMID: 36280213 DOI: 10.1016/j.metabol.2022.155338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Homeostasis of autophagy under normal conditions and nutrient stress is maintained by adaptive activation of regulatory proteins. However, the protein-lipid crosstalk that modulates the switch from suppression to activation of autophagy initiation is largely unknown. RESULTS Here, we show that human diazepam-binding inhibitor (DBI), also known as acyl-CoA binding protein (ACBP), binds to phosphatidylethanolamine of the phagophore membrane under nutrient-rich growth conditions, leading to inhibition of LC3 lipidation and suppression of autophagy initiation. Specific residues, including the conserved tyrosine residues of DBI, interact with phosphatidylethanolamine to stabilize the later molecule in the acyl-CoA binding cavity of the protein. Under starvation, phosphorylation of serine-21 of DBI mediated by the AMP-activated protein kinase results in a drastic reduction in the affinity of the protein for phosphatidylethanolamine. The release of serine-21 phosphorylated DBI from the phagophore upon nutrient starvation restores the high LC3 lipidation flux and maturation of the phagophore to autophagosome. CONCLUSION DBI acts as a strategic barrier against overactivation of phagophore maturation under nutrient-rich conditions, while triggering autophagy under nutrient-deficient conditions.
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Affiliation(s)
- Prajna Udupa
- Departmentof Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Abhishek Kumar
- School of Medicine, University of California, San Francisco, United States of America
| | - Rahul Parit
- Departmentof Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Debasish Kumar Ghosh
- Departmentof Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
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5
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Interactions between plant lipid-binding proteins and their ligands. Prog Lipid Res 2022; 86:101156. [DOI: 10.1016/j.plipres.2022.101156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 10/05/2021] [Accepted: 01/14/2022] [Indexed: 01/11/2023]
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6
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Alquier T, Christian-Hinman CA, Alfonso J, Færgeman NJ. From benzodiazepines to fatty acids and beyond: revisiting the role of ACBP/DBI. Trends Endocrinol Metab 2021; 32:890-903. [PMID: 34565656 PMCID: PMC8785413 DOI: 10.1016/j.tem.2021.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 01/19/2023]
Abstract
Four decades ago Costa and colleagues identified a small, secreted polypeptide in the brain that can displace the benzodiazepine diazepam from the GABAA receptor, and was thus termed diazepam binding inhibitor (DBI). Shortly after, an identical polypeptide was identified in liver by its ability to induce termination of fatty acid synthesis, and was named acyl-CoA binding protein (ACBP). Since then, ACBP/DBI has been studied in parallel without a clear and integrated understanding of its dual roles. The first genetic loss-of-function models have revived the field, allowing targeted approaches to better understand the physiological roles of ACBP/DBI in vivo. We discuss the roles of ACBP/DBI in central and tissue-specific functions in mammals, with an emphasis on metabolism and mechanisms of action.
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Affiliation(s)
- Thierry Alquier
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal Diabetes Research Center, and Departments of Medicine, Pharmacology and Physiology, Biochemistry, and Neurosciences, Université de Montréal, Montreal, QC, Canada.
| | - Catherine A Christian-Hinman
- Department of Molecular and Integrative Physiology, Neuroscience Program, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Julieta Alfonso
- Department of Clinical Neurobiology, University Hospital Heidelberg and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Nils J Færgeman
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
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7
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Kumar A, Ghosh DK, Ranjan A. Differential Stabilities of Mefloquine-Bound Human and Plasmodium falciparum Acyl-CoA-Binding Proteins. ACS OMEGA 2021; 6:1883-1893. [PMID: 33521428 PMCID: PMC7841788 DOI: 10.1021/acsomega.0c04582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/01/2020] [Indexed: 05/03/2023]
Abstract
Toxic effects of pharmacological drugs restrict their robust application against human diseases. Although used as a drug in the combinatorial therapy to treat malaria, the use of mefloquine is not highly recommended because of its adverse effects in humans. Mefloquine inhibits the binding of acyl-CoAs to acyl-CoA-binding proteins of Plasmodium falciparum (PfACBPs) and human (hACBP). In this study, we have used molecular dynamics simulation and other computational approaches to investigate the differences of stabilities of mefloquine-PfACBP749 and mefloquine-hACBP complexes. The stability of mefloquine in the binding cavity of PfACBP749 is less than its stability in the binding pocket of hACBP. Although the essential tyrosine residues (tyrosine-30 and tyrosine-33 of PfACBP749 and tyrosine-29 and tyrosine-32 of hACBP) mediate the initial binding of mefloquine to the proteins by π-stacking interactions, additional temporally longer interactions between mefloquine and aspartate-22 and methionine-25 of hACBP result in stronger binding of mefloquine to hACBP. The higher fluctuation of mefloquine-binding residues of PfACBP749 contributes to the instability of mefloquine in the binding cavity of the protein. On the contrary, in the mefloquine-bound state, the stability of hACBP protein is less than the stability of PfACBP749. The helix-to-coil transition of the N-terminal hydrophobic region of hACBP has a destabilizing effect upon the protein's structure. This causes the induction of aggregation properties in the hACBP in the mefloquine-bound state. Taken together, we describe the mechanistic features that affect the differential dynamic stabilities of mefloquine-bound PfACBP749 and hACBP proteins.
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Affiliation(s)
- Abhishek Kumar
- Computational
and Functional Genomics Group, Centre for
DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana 500039, India
- Graduate
Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Debasish Kumar Ghosh
- Computational
and Functional Genomics Group, Centre for
DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana 500039, India
| | - Akash Ranjan
- Computational
and Functional Genomics Group, Centre for
DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana 500039, India
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8
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Azlan NS, Guo ZH, Yung WS, Wang Z, Lam HM, Lung SC, Chye ML. In silico Analysis of Acyl-CoA-Binding Protein Expression in Soybean. FRONTIERS IN PLANT SCIENCE 2021; 12:646938. [PMID: 33936134 PMCID: PMC8082252 DOI: 10.3389/fpls.2021.646938] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/12/2021] [Indexed: 05/02/2023]
Abstract
Plant acyl-CoA-binding proteins (ACBPs) form a highly conserved protein family that binds to acyl-CoA esters as well as other lipid and protein interactors to function in developmental and stress responses. This protein family had been extensively studied in non-leguminous species such as Arabidopsis thaliana (thale cress), Oryza sativa (rice), and Brassica napus (oilseed rape). However, the characterization of soybean (Glycine max) ACBPs, designated GmACBPs, has remained unreported although this legume is a globally important crop cultivated for its high oil and protein content, and plays a significant role in the food and chemical industries. In this study, 11 members of the GmACBP family from four classes, comprising Class I (small), Class II (ankyrin repeats), Class III (large), and Class IV (kelch motif), were identified. For each class, more than one copy occurred and their domain architecture including the acyl-CoA-binding domain was compared with Arabidopsis and rice. The expression profile, tertiary structure and subcellular localization of each GmACBP were predicted, and the similarities and differences between GmACBPs and other plant ACBPs were deduced. A potential role for some Class III GmACBPs in nodulation, not previously encountered in non-leguminous ACBPs, has emerged. Interestingly, the sole member of Class III ACBP in each of non-leguminous Arabidopsis and rice had been previously identified in plant-pathogen interactions. As plant ACBPs are known to play important roles in development and responses to abiotic and biotic stresses, the in silico expression profiles on GmACBPs, gathered from data mining of RNA-sequencing and microarray analyses, will lay the foundation for future studies in their applications in biotechnology.
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Affiliation(s)
- Nur Syifaq Azlan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ze-Hua Guo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wai-Shing Yung
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Zhili Wang
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Shiu-Cheung Lung
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
- *Correspondence: Shiu-Cheung Lung,
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
- Mee-Len Chye,
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9
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Jin J, Guo ZH, Hao Q, Chye ML. Crystal structure of the rice acyl-CoA-binding protein OsACBP2 in complex with C18:3-CoA reveals a novel pattern of binding to acyl-CoA esters. FEBS Lett 2020; 594:3568-3575. [PMID: 32888212 DOI: 10.1002/1873-3468.13923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/29/2022]
Abstract
Acyl-CoA-binding proteins (ACBPs) are a family of proteins that bind acyl-CoA esters at a conserved acyl-CoA-binding domain. ACBPs maintain intracellular acyl-CoA pools to regulate lipid metabolism. Here, we report on the structure of rice OsACBP2 in complex with C18:3-CoA ester. The residues Y33, K34 and K56 of OsACBP2 play a crucial role in binding the CoA group, while residues N23, L27, K52 and Y55 in one molecule of OsACBP2 cooperate with L27, L28, A59 and A62 from another anchoring the fatty acyl group. Multiangle light scattering assays indicate that OsACBP2 binds C18:3-CoA as a monomer. The first complex structure of a plant ACBP binding with C18:3-CoA is therefore presented, providing a novel model for the interaction between an acyl-CoA ester and the acyl-CoA-binding domain(s).
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Affiliation(s)
- Jing Jin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Ze-Hua Guo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Quan Hao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.,State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, N.T, China
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10
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Tonon MC, Vaudry H, Chuquet J, Guillebaud F, Fan J, Masmoudi-Kouki O, Vaudry D, Lanfray D, Morin F, Prevot V, Papadopoulos V, Troadec JD, Leprince J. Endozepines and their receptors: Structure, functions and pathophysiological significance. Pharmacol Ther 2020; 208:107386. [DOI: 10.1016/j.pharmthera.2019.06.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/20/2019] [Indexed: 02/06/2023]
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11
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Amin M, Samy H, Küpper J. Robust and Accurate Computational Estimation of the Polarizability Tensors of Macromolecules. J Phys Chem Lett 2019; 10:2938-2943. [PMID: 31074620 DOI: 10.1021/acs.jpclett.9b00963] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Alignment of molecules through electric fields minimizes the averaging over orientations, e.g., in single-particle-imaging experiments. The response of molecules to external ac electric fields is governed by their polarizability tensor, which is usually calculated using quantum chemistry methods. These methods are not feasible for large molecules. Here, we calculate the polarizability tensor of proteins using a regression model that correlates the polarizabilities of the 20 amino acids with perfect conductors of the same shape. The dielectric constant of the molecules could be estimated from the slope of the regression line based on the Clausius-Mossotti equation. We benchmark our predictions against the quantum chemistry results for the Trp cagemini protein and the measured dielectric constants of larger proteins. Our method has applications in computing laser alignment of macromolecules, for instance, benefiting single-particle imaging, as well as for estimation of the optical and electrostatic characteristics of proteins and other macromolecules.
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Affiliation(s)
- Muhamed Amin
- Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85 , 22607 Hamburg , Germany
| | - Hebatallah Samy
- University of Science and Technology, Zewail City , 6th of October City, Giza , Egypt
| | - Jochen Küpper
- Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85 , 22607 Hamburg , Germany
- Department of Physics , Universität Hamburg , Luruper Chaussee 149 , 22761 Hamburg , Germany
- Department of Chemistry , Universität Hamburg , Martin-Luther-King-Platz 6 , 20146 Hamburg , Germany
- The Hamburg Center for Ultrafast Imaging , Universität Hamburg , Luruper Chaussee 149 , 22761 Hamburg , Germany
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12
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Kumar A, Ghosh DK, Ali J, Ranjan A. Characterization of Lipid Binding Properties of Plasmodium falciparum Acyl-Coenzyme A Binding Proteins and Their Competitive Inhibition by Mefloquine. ACS Chem Biol 2019; 14:901-915. [PMID: 30986346 DOI: 10.1021/acschembio.9b00003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Malaria remains a worldwide concern in terms of morbidity and mortality. Limited understanding of the Plasmodium proteome makes it challenging to control malaria. Understanding of the expression and functions of different Plasmodium proteins will help in knowing this organism's virulence properties, besides facilitating the drug development process. In this study, we characterize the lipid binding and biophysical properties of the putative Plasmodium falciparum acyl-CoA binding proteins (PfACBPs), which may have intriguing functions in different stages of P. falciparum life cycle. While the PfACBPs can bind to long-chain fatty acyl-CoAs with high affinity, their affinity for short-chain fatty acyl-CoAs is weak. Base-stacking, electrostatic, and hydrophobic interactions between the aromatic rings, charged groups or residues, and hydrophobic chains or residues are responsible for acyl-CoA binding to PfACBPs. PfACBPs can also bind to phospholipids. PfACBPs cannot bind to the fatty acids and unphosphorylated fatty acid esters. PfACBPs are globular-helical proteins that contain a conserved acyl-CoA binding region. They exist in folded or unfolded conformations without attaining any intermediate state. In a systematic high-throughput in silico screening, mefloquine is identified as a potential ligand of PfACBPs. Binding affinities of mefloquine are much higher than those of fatty acyl-CoAs for all PfACBPs. Mefloquine binds to the acyl-CoA binding pocket of PfACBPs, thereby engaging many of the critical residues. Thus, mefloquine acts as a competitive inhibitor against fatty acyl-CoA binding to PfACBPs, leading to the prevention of P. falciparum growth and proliferation. Taken together, our study characterizes the functions of annotated PfACBPs and highlights the mechanistic details of their inactivation by mefloquine.
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Affiliation(s)
- Abhishek Kumar
- Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Uppal, Hyderabad, Telangana 500039, India
- Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Debasish Kumar Ghosh
- Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Uppal, Hyderabad, Telangana 500039, India
- Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Jamshaid Ali
- Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Uppal, Hyderabad, Telangana 500039, India
- Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
- Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram, Kerala 695014, India
| | - Akash Ranjan
- Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Uppal, Hyderabad, Telangana 500039, India
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13
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Identification of possible new salivary biomarkers of stress in sheep using a high-resolution quantitative proteomic technique. Res Vet Sci 2019; 124:338-345. [PMID: 31060013 DOI: 10.1016/j.rvsc.2019.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/30/2019] [Accepted: 04/16/2019] [Indexed: 11/24/2022]
Abstract
The aim of this study was to identify biological pathways and proteins differentially expressed in the saliva proteome of sheep after the application of a model of stress, using high-resolution quantitative proteomics. In addition, one of the proteins differently expressed was verified and evaluated as a possible biomarker of stress in this species. Saliva paired samples from eight sheep before and after the application of a model of stress based on shearing were analysed using tandem mass tags (TMT). The TMT analysis allowed for the identification of new stress-related metabolic pathways and revealed 13 proteins, never described in saliva of sheep, that were differentially expressed between before and after the stress. Six of these proteins pertain to four major metabolic pathways affected, namely: canonical glycolysis, oxygen transport, neural nucleus development, and regulation of actin cytoskeleton reorganization. The rest of proteins were unmapped original proteins such as acyl-coenzyme-A-binding protein; complement C3; alpha-2-macroglobulin isoform-X1; type-II small proline-rich protein; lactoferrin; secretoglobin family-1D-member; and keratin, type-II cytoskeletal 6. Of these proteins, based on its biological significance and specific immunoassay availability, lactoferrin was selected for further validation. The immunoassay intra- and inter-assay coefficients of variation were lower than 13%. The method showed good linearity under dilution and recovery, and the detection limit was low enough to detect salivary lactoferrin levels. A significant decrease (P < 0.01) in salivary lactoferrin concentration in the sheep following the application of the model of stress was observed, suggesting that this protein could be a potential salivary biomarker of stress situations in sheep.
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Raboanatahiry N, Wang B, Yu L, Li M. Functional and Structural Diversity of Acyl-coA Binding Proteins in Oil Crops. Front Genet 2018; 9:182. [PMID: 29872448 PMCID: PMC5972291 DOI: 10.3389/fgene.2018.00182] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 05/01/2018] [Indexed: 12/16/2022] Open
Abstract
Diversities in structure and function of ACBP were discussed in this review. ACBP are important proteins that could transport newly synthesized fatty acid, activated into -coA, from plastid to endoplasmic reticulum, where oil in the form of triacylglycerol occurs. ACBP were detected in various animal and plants species, which indicated their importance in biological function. In fact, involvement of ACBP in important process such as lipid metabolism, regulation of enzyme and gene expression, and in response to plant stresses has been proven in several studies. In this review, findings on ACBP of 11 well-known oil crops were reviewed to comprehend diversity, comparative analyses on ACBP structure were made, and link between structure and function, tissue expression and subcellular location of ACBP were also observed. Incomplete reports in some species were mentioned, which might be encouraging to start or to perform deeper studies. Similar characteristics were found in paralogs ACBP, and orthologs ACBP had different functions, despite the high identity in amino acid sequence. At the end, it is confirmed that ortholog proteins could not necessarily display the same function, even from closely related species.
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Affiliation(s)
- Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
| | - Baoshan Wang
- College of Life Science, Shandong Normal University, Jinan, China
| | - Longjiang Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
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15
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Long C, Liu M, Chen X, Wang X, Ai M, Cui J, Zeng B. The acyl-CoA binding protein affects Monascus pigment production in Monascus ruber CICC41233. 3 Biotech 2018; 8:121. [PMID: 29430382 DOI: 10.1007/s13205-018-1147-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/01/2018] [Indexed: 11/24/2022] Open
Abstract
The present study verified whether acyl-coenzyme A (acyl-CoA)-binding protein (ACBP) affected the production of Monascus pigments (MPs) in Monascus ruber CICC41233 (MrACBP). Phylogenetic analysis revealed that the cloned Mracbp gene, which encoded the MrACBP protein, exhibited the closest match (99% confidence level) to the gene from Penicilliopsis zonata. The MrACBP and maltose-binding protein (MBP) were simultaneously expressed in Escherichia coli Rosetta DE3 in the form of a fusion protein. The microscale thermophoresis binding assay revealed that the purified MBP-MrACBP exhibited a higher affinity for myristoyl-CoA (Kd = 88.16 nM) than for palmitoyl-CoA (Kd = 136.07 nM) and octanoyl-CoA (Kd = 270.9 nM). Further, the Mracbp gene was homologously overexpressed in M. ruber CICC41233, and a positive transformant M. ruber ACBP5 was isolated. The fatty acid myristic acid in M. ruber ACBP5 was lower than that in the parent strain M. ruber CICC41233. However, when compared with the parent strain, the production of total MPs, water-soluble pigment, and ethanol-soluble pigment in M. ruber ACBP5 increased by 11.67, 9.80, and 12.70%, respectively, after 6 days. The relative gene expression level, as determined by a quantitative real-time polymerase chain reaction analysis, of the key genes acbp, pks, mppr1, fasA, and fasB increased by 4.03-, 3.58-, 1.67-, 2.11-, and 2.62-fold after 6 days. These data demonstrate the binding preference of MrACBP for myristoyl-CoA, and its influence on MPs production.
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Affiliation(s)
- Chuannan Long
- 1Jiangxi Key Laboratory of Bioprocess Engineering, Jiangxi Science and Technology Normal University, Nanchang, 330013 People's Republic of China
- 2School of Life Science, Jiangxi Science and Technology Normal University, Nanchang, 330013 People's Republic of China
| | - Mengmeng Liu
- 2School of Life Science, Jiangxi Science and Technology Normal University, Nanchang, 330013 People's Republic of China
| | - Xia Chen
- 2School of Life Science, Jiangxi Science and Technology Normal University, Nanchang, 330013 People's Republic of China
| | - Xiaofang Wang
- 2School of Life Science, Jiangxi Science and Technology Normal University, Nanchang, 330013 People's Republic of China
| | - Mingqiang Ai
- 1Jiangxi Key Laboratory of Bioprocess Engineering, Jiangxi Science and Technology Normal University, Nanchang, 330013 People's Republic of China
- 2School of Life Science, Jiangxi Science and Technology Normal University, Nanchang, 330013 People's Republic of China
| | - Jingjing Cui
- 1Jiangxi Key Laboratory of Bioprocess Engineering, Jiangxi Science and Technology Normal University, Nanchang, 330013 People's Republic of China
| | - Bin Zeng
- 1Jiangxi Key Laboratory of Bioprocess Engineering, Jiangxi Science and Technology Normal University, Nanchang, 330013 People's Republic of China
- 2School of Life Science, Jiangxi Science and Technology Normal University, Nanchang, 330013 People's Republic of China
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16
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Mandalaparthy V, Sanaboyana VR, Rafalia H, Gosavi S. Exploring the effects of sparse restraints on protein structure prediction. Proteins 2017; 86:248-262. [DOI: 10.1002/prot.25438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/20/2017] [Accepted: 11/29/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Varun Mandalaparthy
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road; Bangalore 560065 India
| | - Venkata Ramana Sanaboyana
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road; Bangalore 560065 India
| | - Hitesh Rafalia
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road; Bangalore 560065 India
- Manipal University, Madhav Nagar; Manipal 576104 India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road; Bangalore 560065 India
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17
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Guo ZH, Chan WHY, Kong GKW, Hao Q, Chye ML. The first plant acyl-CoA-binding protein structures: the close homologues OsACBP1 and OsACBP2 from rice. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:438-448. [PMID: 28471368 DOI: 10.1107/s2059798317004193] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/14/2017] [Indexed: 12/13/2022]
Abstract
Acyl-CoA-binding proteins (ACBPs) are a family of proteins that facilitate the binding of long-chain acyl-CoA esters at a conserved acyl-CoA-binding domain. ACBPs act to form intracellular acyl-CoA pools, transport acyl-CoA esters and regulate lipid metabolism. In the model plant Arabidopsis thaliana, a family of six ACBPs has been demonstrated to function in stress and development. Six ACBPs (OsACBPs) have also been identified in Oryza sativa (rice), but they are not as well characterized as those in Arabidopsis thaliana. To understand the need in rice for the two 10 kDa ACBPs, namely OsACBP1 and OsACBP2, which share 79% sequence identity, their crystal structures were elucidated and their affinities toward acyl-CoA esters were compared using isothermal titration calorimetry. OsACBP2 was found to display a higher binding affinity for unsaturated acyl-CoA esters than OsACBP1. A difference between the two proteins is observed at helix 3 and is predicted to lead to different ligand-binding modes in terms of the shape of the binding pocket and the residues that are involved. OsACBP1 thus resembles bovine ACBP, while OsACBP2 is similar to human liver ACBP, in both structure and binding affinity. This is the first time that ACBP structures have been reported from plants, and suggests that OsACBP1 and OsACBP2 are not redundant in function despite their high sequence identity and general structural similarity.
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Affiliation(s)
- Ze Hua Guo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wallace H Y Chan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Geoffrey K W Kong
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Quan Hao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Mee Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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18
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Micheletto MC, Mendes LFS, Basso LGM, Fonseca-Maldonado RG, Costa-Filho AJ. Lipid membranes and acyl-CoA esters promote opposing effects on acyl-CoA binding protein structure and stability. Int J Biol Macromol 2017; 102:284-296. [PMID: 28390829 DOI: 10.1016/j.ijbiomac.2017.03.197] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 12/21/2022]
Abstract
Acyl-CoA Binding Proteins (ACBP) form a housekeeping family of proteins that is responsible for the buffering of long chain acyl-coenzyme A esters (LCFA-CoA) inside the cell. Even though numerous studies have focused on the characterization of different members of the ACBP family, the knowledge about the impact of both LCFA-CoA and phospholipids on ACBP structure and stability remains scarce. Besides, there are still controversies regarding the possible interaction of ACBP with biological membranes, even though this might be essential for the cargo capture and delivery. In this study, we observed that LCFA-CoA and phospholipids play opposite roles on protein stability and that the interaction with the membrane is dictated by electrostatic interaction. Furthermore, the results support the hypothesis that the LCFA-CoA delivery is driven by the increase of the negative charge on the membrane surface. The combined influence played by the different molecules on ACBP structure is discussed on the light of cargo capture/delivery giving new insights about this important process.
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Affiliation(s)
- Mariana C Micheletto
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Luís F S Mendes
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Luis G M Basso
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Raquel G Fonseca-Maldonado
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil; Instituto Federal de Educação, Ciência e Tecnologia de São Paulo/IFSP Campus Jacareí-Dept Gestão, Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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19
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PDB2CD visualises dynamics within protein structures. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:607-616. [PMID: 28374045 PMCID: PMC5599472 DOI: 10.1007/s00249-017-1203-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/13/2017] [Accepted: 02/17/2017] [Indexed: 11/23/2022]
Abstract
Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study. The solution NMR approach invariably results in a cluster of structures whose conformations satisfy the distance boundaries imposed by the data collected; it might be argued that this is evidence of the dynamics of proteins when in solution. In crystal structures, the proteins are often in an energy minimum state which can result in an increase in the extent of regular secondary structure present relative to the solution state depicted by NMR, because the more dynamic ends of alpha helices and beta strands can become ordered at the lower temperatures. This study examines a novel way to display the differences in conformations within an NMR ensemble and between these and a crystal structure of a protein. Circular dichroism (CD) spectroscopy can be used to characterise protein structures in solution. Using the new bioinformatics tool, PDB2CD, which generates CD spectra from atomic resolution protein structures, the differences between, and possible dynamic range of, conformations adopted by a protein can be visualised.
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20
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Aznar-Moreno JA, Venegas-Calerón M, Du ZY, Garcés R, Tanner JA, Chye ML, Martínez-Force E, Salas JJ. Characterization of a small acyl-CoA-binding protein (ACBP) from Helianthus annuus L. and its binding affinities. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 102:141-50. [PMID: 26938582 DOI: 10.1016/j.plaphy.2016.02.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 05/18/2023]
Abstract
Acyl-CoA-binding proteins (ACBPs) bind to acyl-CoA esters and promote their interaction with other proteins, lipids and cell structures. Small class I ACBPs have been identified in different plants, such as Arabidopsis thaliana (AtACBP6), Brassica napus (BnACBP) and Oryza sativa (OsACBP1, OsACBP2, OsACBP3), and they are capable of binding to different acyl-CoA esters and phospholipids. Here we characterize HaACBP6, a class I ACBP expressed in sunflower (Helianthus annuus) tissues, studying the specificity of its corresponding recombinant HaACBP6 protein towards various acyl-CoA esters and phospholipids in vitro, particularly using isothermal titration calorimetry and protein phospholipid binding assays. This protein binds with high affinity to de novo synthetized derivatives palmitoly-CoA, stearoyl-CoA and oleoyl-CoA (Kd 0.29, 0.14 and 0.15 μM respectively). On the contrary, it showed lower affinity towards linoleoyl-CoA (Kd 5.6 μM). Moreover, rHaACBP6 binds to different phosphatidylcholine species (dipalmitoyl-PC, dioleoyl-PC and dilinoleoyl-PC), yet it displays no affinity towards other phospholipids like lyso-PC, phosphatidic acid and lysophosphatidic acid derivatives. In the light of these results, the possible involvement of this protein in sunflower oil synthesis is considered.
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Affiliation(s)
- Jose A Aznar-Moreno
- Department of Biochemistry & Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS 66506
| | - Mónica Venegas-Calerón
- Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Ctra. de Utrera Km 1, 41013 Seville, Spain
| | - Zhi-Yan Du
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Rafael Garcés
- Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Ctra. de Utrera Km 1, 41013 Seville, Spain
| | - Julian A Tanner
- Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Enrique Martínez-Force
- Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Ctra. de Utrera Km 1, 41013 Seville, Spain
| | - Joaquín J Salas
- Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Ctra. de Utrera Km 1, 41013 Seville, Spain.
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Abstract
Acyl-CoA-binding proteins (ACBPs) play a pivotal role in fatty acid metabolism because they can transport medium- and long-chain acyl-CoA esters. In eukaryotic cells, ACBPs are involved in intracellular trafficking of acyl-CoA esters and formation of a cytosolic acyl-CoA pool. In addition to these ubiquitous functions, more specific non-redundant roles of plant ACBP subclasses are implicated by the existence of multigene families with variable molecular masses, ligand specificities, functional domains (e.g. protein-protein interaction domains), subcellular locations and gene expression patterns. In this chapter, recent progress in the characterization of ACBPs from the model dicot plant, Arabidopsis thaliana, and the model monocot, Oryza sativa, and their emerging roles in plant growth and development are discussed. The functional significance of respective members of the plant ACBP families in various developmental and physiological processes such as seed development and germination, stem cuticle formation, pollen development, leaf senescence, peroxisomal fatty acid β-oxidation and phloem-mediated lipid transport is highlighted.
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Affiliation(s)
- Shiu-Cheung Lung
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
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22
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Lung SC, Chye ML. The binding versatility of plant acyl-CoA-binding proteins and their significance in lipid metabolism. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1861:1409-1421. [PMID: 26747650 DOI: 10.1016/j.bbalip.2015.12.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 12/28/2015] [Accepted: 12/29/2015] [Indexed: 11/18/2022]
Abstract
Acyl-CoA esters are the activated form of fatty acids and play important roles in lipid metabolism and the regulation of cell functions. They are bound and transported by nonenzymic proteins such as the acyl-CoA-binding proteins (ACBPs). Although plant ACBPs were so named by virtue of amino acid homology to existing yeast and mammalian counterparts, recent studies revealed that ligand specificities of plant ACBPs are not restricted to acyl-CoA esters. Arabidopsis and rice ACBPs also interact with phospholipids, and their affinities to different acyl-CoA species and phospholipid classes vary amongst isoforms. Their ligands also include heavy metals. Interactors of plant ACBPs are further diversified due to the evolution of protein-protein interacting domains. This review summarizes our current understanding of plant ACBPs with a focus on their binding versatility. Their broad ligand range is of paramount significance in serving a multitude of functions during development and stress responses as discussed herein. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.
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Affiliation(s)
- Shiu-Cheung Lung
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
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23
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Hao Q, Liu X, Zhao G, Jiang L, Li M, Zeng B. Recombinant expression, purification, and characterization of an acyl-CoA binding protein from Aspergillus oryzae. Biotechnol Lett 2015; 38:519-25. [DOI: 10.1007/s10529-015-2003-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/13/2015] [Indexed: 11/28/2022]
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Neess D, Bek S, Engelsby H, Gallego SF, Færgeman NJ. Long-chain acyl-CoA esters in metabolism and signaling: Role of acyl-CoA binding proteins. Prog Lipid Res 2015; 59:1-25. [PMID: 25898985 DOI: 10.1016/j.plipres.2015.04.001] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/11/2015] [Accepted: 04/09/2015] [Indexed: 02/03/2023]
Abstract
Long-chain fatty acyl-CoA esters are key intermediates in numerous lipid metabolic pathways, and recognized as important cellular signaling molecules. The intracellular flux and regulatory properties of acyl-CoA esters have been proposed to be coordinated by acyl-CoA-binding domain containing proteins (ACBDs). The ACBDs, which comprise a highly conserved multigene family of intracellular lipid-binding proteins, are found in all eukaryotes and ubiquitously expressed in all metazoan tissues, with distinct expression patterns for individual ACBDs. The ACBDs are involved in numerous intracellular processes including fatty acid-, glycerolipid- and glycerophospholipid biosynthesis, β-oxidation, cellular differentiation and proliferation as well as in the regulation of numerous enzyme activities. Little is known about the specific roles of the ACBDs in the regulation of these processes, however, recent studies have gained further insights into their in vivo functions and provided further evidence for ACBD-specific functions in cellular signaling and lipid metabolic pathways. This review summarizes the structural and functional properties of the various ACBDs, with special emphasis on the function of ACBD1, commonly known as ACBP.
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Affiliation(s)
- Ditte Neess
- Villum Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Signe Bek
- Villum Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Hanne Engelsby
- Villum Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Sandra F Gallego
- Villum Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Nils J Færgeman
- Villum Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark.
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25
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Onwukwe GU, Kursula P, Koski MK, Schmitz W, Wierenga RK. Human Δ3,Δ2-enoyl-CoA isomerase, type 2: a structural enzymology study on the catalytic role of its ACBP domain and helix-10. FEBS J 2015; 282:746-68. [DOI: 10.1111/febs.13179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Goodluck U. Onwukwe
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine; University of Oulu; Finland
| | - Petri Kursula
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine; University of Oulu; Finland
- Department of Biomedicine; University of Bergen; Norway
| | - M. Kristian Koski
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine; University of Oulu; Finland
| | - Werner Schmitz
- Theodor Boveri Institute of Biosciences (Biocenter); University of Würzburg; Germany
| | - Rik K. Wierenga
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine; University of Oulu; Finland
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26
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Arabidopsis cytosolic acyl-CoA-binding proteins ACBP4, ACBP5 and ACBP6 have overlapping but distinct roles in seed development. Biosci Rep 2014; 34:e00165. [PMID: 25423293 PMCID: PMC4274664 DOI: 10.1042/bsr20140139] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Eukaryotic cytosolic ACBPs (acyl-CoA-binding proteins) bind acyl-CoA esters and maintain a cytosolic acyl-CoA pool, but the thermodynamics of their protein–lipid interactions and physiological relevance in plants are not well understood. Arabidopsis has three cytosolic ACBPs which have been identified as AtACBP4, AtACBP5 and AtACBP6, and microarray data indicated that all of them are expressed in seeds; AtACBP4 is expressed in early embryogenesis, whereas AtACBP5 is expressed later. ITC (isothermal titration calorimetry) in combination with transgenic Arabidopsis lines were used to investigate the roles of these three ACBPs from Arabidopsis thaliana. The dissociation constants, stoichiometry and enthalpy change of AtACBP interactions with various acyl-CoA esters were determined using ITC. Strong binding of recombinant (r) AtACBP6 with long-chain acyl-CoA (C16- to C18-CoA) esters was observed with dissociation constants in the nanomolar range. However, the affinity of rAtACBP4 and rAtACBP5 to these acyl-CoA esters was much weaker (dissociation constants in the micromolar range), suggesting that they interact with acyl-CoA esters differently from rAtACBP6. When transgenic Arabidopsis expressing AtACBP6pro::GUS was generated, strong GUS (β-glucuronidase) expression in cotyledonary-staged embryos and seedlings prompted us to measure the acyl-CoA contents of the acbp6 mutant. This mutant accumulated higher levels of C18:1-CoA and C18:1- and C18:2-CoAs in cotyledonary-staged embryos and seedlings, respectively, in comparison with the wild type. The acbp4acbp5acbp6 mutant showed the lightest seed weight and highest sensitivity to abscisic acid during germination, suggesting their physiological functions in seeds. The binding affinities of the three Arabidopsis cytosolic ACBPs (AtACBP4, AtACBP5 and AtACBP6) with acyl-CoA esters were investigated by ITC. When the biological significance of these AtACBPs was analysed using mutants, results indicated their overlapping functions in seed acyl-lipid metabolism.
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Pastor S, Sethumadhavan K, Ullah AHJ, Gidda S, Cao H, Mason C, Chapital D, Scheffler B, Mullen R, Dyer J, Shockey J. Molecular properties of the class III subfamily of acyl-coenyzme A binding proteins from tung tree (Vernicia fordii). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 203-204:79-88. [PMID: 23415331 DOI: 10.1016/j.plantsci.2012.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 12/14/2012] [Accepted: 12/20/2012] [Indexed: 06/01/2023]
Abstract
Acyl-CoA binding proteins (ACBPs) have been identified in most branches of life, and play various roles in lipid metabolism, among other functions. Plants contain multiple classes of ACBP genes. The most diverse group is the class III proteins. Tung tree (Vernicia fordii) contains two such genes, designated VfACBP3A and VfACBP3B. The two proteins are significantly different in length and sequence. Analysis of tung ACBP3 genes revealed significant evolution, suggesting relatively ancient divergence of the two genes from a common ancestor. Phylogenetic comparisons of multiple plant class III proteins suggest that this group is the most evolutionarily dynamic class of ACBP. Both tung ACBP3 genes are expressed at similar levels in most tissues tested, but ACBP3A is stronger in leaves. Three-dimensional modeling predictions confirmed the presence of the conserved four α-helix bundle acyl-CoA binding (ACB); however, other regions of these proteins likely fold much differently. Acyl-CoA binding assays revealed different affinities for different acyl-CoAs, possibly contradicting the redundancy of function suggested by the gene expression studies. Subcellular targeting of transiently-expressed plant ACBP3 proteins contradicted earlier studies, and suggested that at least some class III ACBPs may be predominantly targeted to endoplasmic reticulum membranes, with little or no targeting to the apoplast.
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Affiliation(s)
- Steven Pastor
- Southern Regional Research Center, United States Department of Agriculture-Agricultural Research Service, 1100 Robert E. Lee Blvd., New Orleans, LA 70124, USA
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Muda HM, Saad P, Othman RM. Remote protein homology detection and fold recognition using two-layer support vector machine classifiers. Comput Biol Med 2011; 41:687-99. [PMID: 21704312 DOI: 10.1016/j.compbiomed.2011.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 03/16/2011] [Accepted: 06/05/2011] [Indexed: 02/07/2023]
Abstract
Remote protein homology detection and fold recognition refer to detection of structural homology in proteins where there are small or no similarities in the sequence. To detect protein structural classes from protein primary sequence information, homology-based methods have been developed, which can be divided to three types: discriminative classifiers, generative models for protein families and pairwise sequence comparisons. Support Vector Machines (SVM) and Neural Networks (NN) are two popular discriminative methods. Recent studies have shown that SVM has fast speed during training, more accurate and efficient compared to NN. We present a comprehensive method based on two-layer classifiers. The 1st layer is used to detect up to superfamily and family in SCOP hierarchy using optimized binary SVM classification rules. It used the kernel function known as the Bio-kernel, which incorporates the biological information in the classification process. The 2nd layer uses discriminative SVM algorithm with string kernel that will detect up to protein fold level in SCOP hierarchy. The results obtained were evaluated using mean ROC and mean MRFP and the significance of the result produced with pairwise t-test was tested. Experimental results show that our approaches significantly improve the performance of remote protein homology detection and fold recognition for all three different version SCOP datasets (1.53, 1.67 and 1.73). We achieved 4.19% improvements in term of mean ROC in SCOP 1.53, 4.75% in SCOP 1.67 and 4.03% in SCOP 1.73 datasets when compared to the result produced by well-known methods. The combination of first layer and second layer of BioSVM-2L performs well in remote homology detection and fold recognition even in three different versions of datasets.
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Affiliation(s)
- Hilmi M Muda
- Laboratory of Computational Intelligence and Biology, Faculty of Computer Science and Information Systems, Universiti Teknologi Malaysia, 81310 UTM Skudai, Malaysia
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29
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Yurchenko OP, Weselake RJ. Involvement of low molecular mass soluble acyl-CoA-binding protein in seed oil biosynthesis. N Biotechnol 2010; 28:97-109. [PMID: 20933624 DOI: 10.1016/j.nbt.2010.09.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Revised: 09/11/2010] [Accepted: 09/29/2010] [Indexed: 01/03/2023]
Abstract
Acyl-CoA-binding protein (ACBP), a low molecular mass (m) (∼ 10 kDa) soluble protein ubiquitous in eukaryotes, plays an important housekeeping role in lipid metabolism by maintaining the intracellular acyl-CoA pool. ACBP is involved in lipid biosynthesis and transport, gene expression, and membrane biogenesis. In plants, low m ACBP and high m ACBPs participate in response mechanisms to biotic and abiotic factors, acyl-CoA transport in phloem, and biosynthesis of structural and storage lipids. In light of current research on the modification of seed oil, insight into mechanisms of substrate trafficking within lipid biosynthetic pathways is crucial for developing rational strategies for the production of specialty oils with the desired alterations in fatty acid composition. In this review, we summarize our knowledge of plant ACBPs with emphasis on the role of low m ACBP in seed oil biosynthesis, based on in vitro studies and analyses of transgenic plants. Future prospects and possible applications of low m ACBP in seed oil modification are discussed.
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Affiliation(s)
- Olga P Yurchenko
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta, Canada
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30
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Déchamps S, Shastri S, Wengelnik K, Vial HJ. Glycerophospholipid acquisition in Plasmodium - a puzzling assembly of biosynthetic pathways. Int J Parasitol 2010; 40:1347-65. [PMID: 20600072 DOI: 10.1016/j.ijpara.2010.05.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2010] [Revised: 05/24/2010] [Accepted: 05/25/2010] [Indexed: 01/06/2023]
Abstract
Throughout the Plasmodium life cycle, malaria parasites repeatedly undergo rapid cellular growth and prolific divisions, necessitating intense membrane neogenesis and, in particular, the acquisition of high amounts of phospholipids. At the intraerythrocytic stage, glycerophospholipids are the main parasite membrane constituents, which mostly originate from the Plasmodium-encoded enzymatic machinery. Several proteins and entire pathways have been characterized and their features reported, thereby generating a global view of glycerophospholipid synthesis across Plasmodium spp. The malaria parasite displays a panoply of pathways that are seldom found together in a single organism. The major glycerophospholipids are synthesized via ancestral prokaryotic CDP-diacylglycerol-dependent pathways and eukaryotic-type de novo pathways. The parasite exhibits additional reactions that bridge some of these routes and are otherwise restricted to some organisms, such as plants, while base-exchange mechanisms are largely unexplored in Plasmodium. Marked differences between Plasmodium spp. have also been reported in phosphatidylcholine and phosphatidylethanolamine synthesis. Little is currently known about glycerophospholipid acquisition at non-erythrocytic stages, but recent data reveal that intrahepatocytic parasites, oocysts and sporozoites import various host lipids, and that de novo fatty acid synthesis is only crucial at the late liver stage. More studies on the different Plasmodium developmental stages are needed, to further assemble the different pieces of this glycerophospholipid synthesis puzzle, which contains highly promising therapeutic targets.
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Affiliation(s)
- Sandrine Déchamps
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, Centre National de la Recherche Scientifique (CNRS) - Universite Montpellier 2, cc 107, Place Eugene Bataillon, 34095 Montpellier Cedex 05, France
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31
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Monzani PS, Pereira HM, Melo FA, Meirelles FV, Oliva G, Cascardo JCM. A new topology of ACBP from Moniliophthora perniciosa. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:115-23. [PMID: 19782157 DOI: 10.1016/j.bbapap.2009.09.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 09/11/2009] [Accepted: 09/16/2009] [Indexed: 10/20/2022]
Abstract
Acyl-CoA binding protein (ACBP) is a housekeeping protein and is an essential protein in human cell lines and in Trypanosoma brucei. The ACBP of Moniliophthora perniciosa is composed of 104 amino acids and is possibly a non-classic isoform exclusively from Basidiomycetes. The M. perniciosa acbp gene was cloned, and the protein was expressed and purified. Acyl-CoA ester binding was analyzed by isoelectric focusing, native gel electrophoresis and isothermal titration calorimetry. Our results suggest an increasing affinity of ACBP for longer acyl-CoA esters, such as myristoyl-CoA to arachidoyl-CoA, and best fit modeling indicates two binding sites. ACBP undergoes a shift from a monomeric to a dimeric state, as shown by dynamic light scattering, fluorescence anisotropy and native gel electrophoresis in the absence and presence of the ligand. The protein's structure was determined at 1.6 A resolution and revealed a new topology for ACBP, containing five alpha-helices instead of four. alpha-helices 1, 2, 3 and 4 adopted a bundled arrangement that is unique from the previously determined four-helix folds of ACBP, while alpha-helices 1, 2, 4 and 5 formed a classical four-helix bundle. A MES molecule was found in the CoA binding site, suggesting that the CoA site could be a target for small compound screening.
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Affiliation(s)
- Paulo S Monzani
- Departamento de Ciências Biológicas, Laboratório de Proteômica, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Ilhéus, BA, CEP 45662-900, Brazil
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32
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Vallejo DF, Zamarreño F, Guérin DMA, Grigera JR, Costabel MD. Prediction of the most favorable configuration in the ACBP-membrane interaction based on electrostatic calculations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1788:696-700. [PMID: 19150435 DOI: 10.1016/j.bbamem.2008.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 12/01/2008] [Accepted: 12/10/2008] [Indexed: 11/19/2022]
Abstract
Acyl-CoA binding proteins (ACBPs) are highly conserved 10 kDa cytosolic proteins that bind medium- and long-chain acyl-CoA esters. They act as intracellular carriers of acyl-CoA and play a role in acyl-CoA metabolism, gene regulation, acyl-CoA-mediated cell signaling, transport-mediated lipid synthesis, membrane trafficking and also, ACBPs were indicated as a possible inhibitor of diazepam binding to the GABA-A receptor. To estimate the importance of the non-specific electrostatic energy in the ACBP-membrane interaction, we computationally modeled the interaction of HgACBP with both anionic and neutral membranes. To compute the Free Electrostatic Energy of Binding (dE), we used the Finite Difference Poisson Boltzmann Equation (FDPB) method as implemented in APBS. In the most energetically favorable orientation, ACBP brings charged residues Lys18 and Lys50 and hydrophobic residues Met46 and Leu47 into membrane surface proximity. This conformation suggests that these four ACBP amino acids are most likely to play a leading role in the ACBP-membrane interaction and ligand intake. Thus, we propose that long range electrostatic forces are the first step in the interaction mechanism between ACBP and membranes.
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Affiliation(s)
- Diego F Vallejo
- Instituto de Física de Líquidos y Sistemas Biológicos (IFLYSIB) CCT La Plata- CONICET- UNLP-CIC, La Plata, Argentina
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33
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Abstract
Advances over the past few years have begun to enable prediction and design of macromolecular structures at near-atomic accuracy. Progress has stemmed from the development of reasonably accurate and efficiently computed all-atom potential functions as well as effective conformational sampling strategies appropriate for searching a highly rugged energy landscape, both driven by feedback from structure prediction and design tests. A unified energetic and kinematic framework in the Rosetta program allows a wide range of molecular modeling problems, from fibril structure prediction to RNA folding to the design of new protein interfaces, to be readily investigated and highlights areas for improvement. The methodology enables the creation of novel molecules with useful functions and holds promise for accelerating experimental structural inference. Emerging connections to crystallographic phasing, NMR modeling, and lower-resolution approaches are described and critically assessed.
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Affiliation(s)
- Rhiju Das
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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34
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Oswald C, Smits SHJ, Bremer E, Schmitt L. Microseeding - a powerful tool for crystallizing proteins complexed with hydrolyzable substrates. Int J Mol Sci 2008; 9:1131-1141. [PMID: 19325794 PMCID: PMC2635726 DOI: 10.3390/ijms9071131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2008] [Revised: 06/05/2008] [Accepted: 06/10/2008] [Indexed: 11/28/2022] Open
Abstract
Hydrolysis is an often-encountered obstacle in the crystallization of proteins complexed with their substrates. As the duration of the crystallization process, from nucleation to the growth of the crystal to its final size, commonly requires several weeks, non-enzymatic hydrolysis of an “unstable” ligand occurs frequently. In cases where the crystallization conditions exhibit non neutral pH values this hydrolysis phenomenon may be even more pronounced. ChoX, the substrate binding protein of a choline ABC-importer, produced crystals with its substrate acetylcholine after one month. However, these crystals exhibited only choline, an acetylcholine hydrolysis product, in the binding site. To overcome this obstacle we devised a microseeding protocol leading to crystals of ChoX with bound acetylcholine within 24 hours. One drawback we encountered was the high twinning fraction of the crystals, possibly was due to the rapid crystal growth.
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Affiliation(s)
- Christine Oswald
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| | - Sander H. J. Smits
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps University Marbrug, Karl-von-Frisch Str., 35032 Marburg, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
- Author to whom correspondence should be addressed: Tel. +49-211-81-10773; Fax: +49-211-81-15310; E-mail:
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35
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Vallejo DFG, Grigera JR, Costabel MD. A hydrophobic loop in acyl-CoA binding protein is functionally important for binding to palmitoyl-coenzyme A: a molecular dynamics study. Int J Biol Macromol 2007; 42:271-7. [PMID: 18242688 DOI: 10.1016/j.ijbiomac.2007.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 12/08/2007] [Accepted: 12/10/2007] [Indexed: 11/27/2022]
Abstract
Acyl-CoA binding protein (ACBP) plays a key role in lipid metabolism, interacting via a partly unknown mechanism with high affinity with long chain fatty acyl-CoAs (LCFA-CoAs). At present there is no study of the microscopic way ligand binding is accomplished. We analyzed this process by molecular dynamics (MDs) simulations. We proposed a computational model of ligand, able to reproduce some evidence from nuclear magnetic resonance (NMR) data, quantitative time resolved fluorometry and X-ray crystallography. We found that a hydrophobic loop, not in the active site, is important for function. Besides, multiple sequence alignment shows hydrophobicity (and not the residues itselves) conservation.
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Affiliation(s)
- Diego F G Vallejo
- Instituto de Física de Líquidos y Sistemas Biológicos (IFLYSIB), UNLP-CONICET-CIC, Argentina
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36
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Faergeman NJ, Wadum M, Feddersen S, Burton M, Kragelund BB, Knudsen J. Acyl-CoA binding proteins; structural and functional conservation over 2000 MYA. Mol Cell Biochem 2007; 299:55-65. [PMID: 17013545 DOI: 10.1007/s11010-005-9040-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Besides serving as essential substrates for beta-oxidation and synthesis of triacylglycerols and more complex lipids like sphingolipids and sterol esters, long-chain fatty acyl-CoA esters are increasingly being recognized as important regulators of enzyme activities and gene transcription. Acyl-CoA binding protein, ACBP, has been proposed to play a pivotal role in the intracellular trafficking and utilization of long-chain fatty acyl-CoA esters. Depletion of acyl-CoA binding protein in yeast results in aberrant organelle morphology incl. fragmented vacuoles, multi-layered plasma membranes and accumulation of vesicles of variable sizes. In contrast to synthesis and turn-over of glycerolipids, the levels of very-long-chain fatty acids, long-chain bases and ceramide are severely affected by Acb1p depletion, suggesting that Acb1p, rather than playing a general role, serves specific roles in cellular lipid metabolism.
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Affiliation(s)
- Nils J Faergeman
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.
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37
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Taskinen JP, van Aalten DM, Knudsen J, Wierenga RK. High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl-CoA ligand. Proteins 2007; 66:229-38. [PMID: 17044054 DOI: 10.1002/prot.21124] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The acyl-CoA binding protein (ACBP) is essential for the fatty acid metabolism, membrane structure, membrane fusion, and ceramide synthesis. Here high resolution crystal structures of human cytosolic liver ACBP, unliganded and liganded with a physiological ligand, myristoyl-CoA are described. The binding of the acyl-CoA molecule induces only few structural differences near the binding pocket. The crystal form of the liganded ACBP, which has two ACBP molecules in the asymmetric unit, shows that in human ACBP the same acyl-CoA binding pocket is present as previously described for the bovine and Plasmodium falciparum ACBP and the mode of binding of the 3'-phosphate-AMP moiety is conserved. Unexpectedly, in one of the acyl-CoA binding pockets the acyl moiety is bound in a reversed mode as compared with the bovine and P. falciparum structures. In this binding mode, the myristoyl-CoA molecule is fully ordered and bound across the two ACBP molecules of the crystallographic asymmetric unit: the 3'-phosphate-AMP moiety is bound in the binding pocket of one ACBP molecule and the acyl chain is bound in the pocket of the other ACBP molecule. The remaining binding pocket cavities of these two ACBP molecules are filled by other ligand fragments. This novel binding mode shows that the acyl moiety can flip out of its classical binding pocket and bind elsewhere, suggesting a mechanism for the acyl-CoA transfer between ACBP and the active site of a target enzyme. This mechanism is of possible relevance for the in vivo function of ACBP.
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Affiliation(s)
- Jukka P Taskinen
- Biocenter Oulu and Department of Biochemistry, University of Oulu, FIN-90014, Finland
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38
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Costabel MD, Ermácora MR, Santomé JA, Alzari PM, Guérin DMA. Structure of armadillo ACBP: a new member of the acyl-CoA-binding protein family. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:958-61. [PMID: 17012783 PMCID: PMC2225200 DOI: 10.1107/s1744309106038164] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Accepted: 09/18/2006] [Indexed: 11/10/2022]
Abstract
The X-ray structure of the tetragonal form of apo acyl-CoA-binding protein (ACBP) from the Harderian gland of the South American armadillo Chaetophractus villosus has been solved. ACBP is a carrier for activated long-chain fatty acids and has been associated with many aspects of lipid metabolism. Its secondary structure is highly similar to that of the corresponding form of bovine ACBP and exhibits the unique flattened alpha-helical bundle (up-down-down-up) motif reported for animal, yeast and insect ACBPs. Conformational differences are located in loops and turns, although these structural differences do not suffice to account for features that could be related to the unusual biochemistry and lipid metabolism of the Harderian gland.
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Affiliation(s)
- Marcelo D Costabel
- Grupo de Biofísica, Departamento de Física, Universidad Nacional del Sur, Bahía Blanca, Argentina.
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39
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Zeng B, Cai X, Zhu G. Functional characterization of a fatty acyl-CoA-binding protein (ACBP) from the apicomplexan Cryptosporidium parvum. MICROBIOLOGY-SGM 2006; 152:2355-2363. [PMID: 16849800 PMCID: PMC1513434 DOI: 10.1099/mic.0.28944-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this paper, the identification and functional analysis of a fatty acyl-CoA-binding protein (ACBP) gene from the opportunistic protist Cryptosporidium parvum are described. The CpACBP1 gene encodes a protein of 268 aa that is three times larger than typical ACBPs (i.e. approximately 90 aa) of humans and animals. Sequence analysis indicated that the CpACBP1 protein consists of an N-terminal ACBP domain (approximately 90 aa) and a C-terminal ankyrin repeat sequence (approximately 170 aa). The entire CpACBP1 ORF was engineered into a maltose-binding protein fusion system and expressed as a recombinant protein for functional analysis. Acyl-CoA-binding assays clearly revealed that the preferred binding substrate for CpACBP1 is palmitoyl-CoA. RT-PCR, Western blotting and immunolabelling analyses clearly showed that the CpACBP1 gene is mainly expressed during the intracellular developmental stages and that the level increases during parasite development. Immunofluorescence microscopy showed that CpACBP1 is associated with the parasitophorous vacuole membrane (PVM), which implies that this protein may be involved in lipid remodelling in the PVM, or in the transport of fatty acids across the membrane.
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Affiliation(s)
- Bin Zeng
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, 4467 TAMU, College Station, TX 77483-4467, USA
| | - Xiaomin Cai
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, 4467 TAMU, College Station, TX 77483-4467, USA
| | - Guan Zhu
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, 4467 TAMU, College Station, TX 77483-4467, USA
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40
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Larsen MK, Tuck S, Færgeman NJ, Knudsen J. MAA-1, a novel acyl-CoA-binding protein involved in endosomal vesicle transport in Caenorhabditis elegans. Mol Biol Cell 2006; 17:4318-29. [PMID: 16870706 PMCID: PMC1635345 DOI: 10.1091/mbc.e06-01-0035] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The budding and fission of vesicles during membrane trafficking requires many proteins, including those that coat the vesicles, adaptor proteins that recruit components of the coat, and small GTPases that initiate vesicle formation. In addition, vesicle formation in vitro is promoted by the hydrolysis of acyl-CoA lipid esters. The mechanisms by which these lipid esters are directed to the appropriate membranes in vivo, and their precise roles in vesicle biogenesis, are not yet understood. Here, we present the first report on membrane associated ACBP domain-containing protein-1 (MAA-1), a novel membrane-associated member of the acyl-CoA-binding protein family. We show that in Caenorhabditis elegans, MAA-1 localizes to intracellular membrane organelles in the secretory and endocytic pathway and that mutations in maa-1 reduce the rate of endosomal recycling. A lack of maa-1 activity causes a change in endosomal morphology. Although in wild type, many endosomal organelles have long tubular protrusions, loss of MAA-1 activity results in loss of the tubular domains, suggesting the maa-1 is required for the generation or maintenance of these domains. Furthermore, we demonstrate that MAA-1 binds fatty acyl-CoA in vitro and that this ligand-binding ability is important for its function in vivo. Our results are consistent with a role for MAA-1 in an acyl-CoA-dependent process during vesicle formation.
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Affiliation(s)
- Morten K. Larsen
- *Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark; and
- Umeå Center for Molecular Pathogenesis, Umeå University, Umeå, SE-90187, Sweden
| | - Simon Tuck
- Umeå Center for Molecular Pathogenesis, Umeå University, Umeå, SE-90187, Sweden
| | - Nils J. Færgeman
- *Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark; and
| | - Jens Knudsen
- *Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark; and
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41
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Abstract
Acyl-CoA-binding protein (ACBP) is a 10 kDa protein that binds C12-C22 acyl-CoA esters with high affinity. In vitro and in vivo experiments suggest that it is involved in multiple cellular tasks including modulation of fatty acid biosynthesis, enzyme regulation, regulation of the intracellular acyl-CoA pool size, donation of acyl-CoA esters for beta-oxidation, vesicular trafficking, complex lipid synthesis and gene regulation. In the present study, we delineate the evolutionary history of ACBP to get a complete picture of its evolution and distribution among species. ACBP homologues were identified in all four eukaryotic kingdoms, Animalia, Plantae, Fungi and Protista, and eleven eubacterial species. ACBP homologues were not detected in any other known bacterial species, or in archaea. Nearly all of the ACBP-containing bacteria are pathogenic to plants or animals, suggesting that an ACBP gene could have been acquired from a eukaryotic host by horizontal gene transfer. Many bacterial, fungal and higher eukaryotic species only harbour a single ACBP homologue. However, a number of species, ranging from protozoa to vertebrates, have evolved two to six lineage-specific paralogues through gene duplication and/or retrotransposition events. The ACBP protein is highly conserved across phylums, and the majority of ACBP genes are subjected to strong purifying selection. Experimental evidence indicates that the function of ACBP has been conserved from yeast to humans and that the multiple lineage-specific paralogues have evolved altered functions. The appearance of ACBP very early on in evolution points towards a fundamental role of ACBP in acyl-CoA metabolism, including ceramide synthesis and in signalling.
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Affiliation(s)
- Mark Burton
- *Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Timothy M. Rose
- †Department of Pathobiology, School of Public Health and Community Medicine, University of Washington, Seattle, WA, 98195, U.S.A
| | - Nils J. Færgeman
- *Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jens Knudsen
- *Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
- To whom correspondence should be addressed (email )
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42
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Schroeder F, Huang H, Hostetler HA, Petrescu AD, Hertz R, Bar-Tana J, Kier AB. Stability of fatty acyl-coenzyme A thioester ligands of hepatocyte nuclear factor-4alpha and peroxisome proliferator-activated receptor-alpha. Lipids 2005; 40:559-68. [PMID: 16149734 DOI: 10.1007/s11745-005-1416-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although long-chain fatty acyl-coenzyme A (LCFA-CoA) thioesters are specific high-affinity ligands for hepatocyte nuclear factor-4alpha (HNF-4alpha) and peroxisome proliferator-activated receptor-alpha (PPARalpha), X-ray crystals of the respective purified recombinant ligand-binding domains (LBD) do not contain LCFA-CoA, but instead exhibit bound LCFA or have lost all ligands during the purification process, respectively. As shown herein: (i) The acyl chain composition of LCFA bound to recombinant HNF-4alpha reflected that of the bacterial LCFA-CoA pool, rather than the bacterial LCFA pool. (ii) Bacteria used to produce the respective HNF-4alpha and PPARalpha contained nearly 100-fold less LCFA-CoA than LCFA. (iii) Under conditions used to crystallize LBD (at least 3 wk at room temperature in aqueous buffer), 16:1-CoA was very unstable in buffer alone. (iv) In the presence of the respective nuclear receptor (i.e., HNF-4alpha and PPARalpha), LBD 70-75% of 16:1-CoA was degraded after 1 d at room temperature in the crystallization buffer, whereas as much as 94-97% of 16:1-CoA was degraded by 3 wk. (v) Cytoplasmic LCFA-CoA binding proteins such as acyl-CoA binding protein, sterol carrier protein-2, and liver-FA binding protein slowed the process of 16:1-CoA degradation proportional to their respective affinities for this ligand. Taken together, these data for the first time indicated that the absence of LCFA-CoA in the crystallized HNF-4alpha and PPARalpha was due to the paucity of LCFA-CoA in bacteria as well as to the instability of LCFA-CoA in aqueous buffers and the conditions used for LBD crystallization. Furthermore, instead of protecting bound LCFA-CoA from autohydrolysis like several cytoplasmic LCFA-CoA binding proteins, these nuclear receptors facilitated LCFA-CoA degradation.
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Affiliation(s)
- Friedhelm Schroeder
- Department of Physiology and Pharmacology, Texas A&M University, TVMC, College Station, Texas 77843-4467, USA
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43
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Teilum K, Thormann T, Caterer NR, Poulsen HI, Jensen PH, Knudsen J, Kragelund BB, Poulsen FM. Different secondary structure elements as scaffolds for protein folding transition states of two homologous four-helix bundles. Proteins 2005; 59:80-90. [PMID: 15690348 DOI: 10.1002/prot.20340] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comparison of the folding processes for homologue proteins can provide valuable information about details in the interactions leading to the formation of the folding transition state. Here the folding kinetics of 18 variants of yACBP and 3 variants of bACBP have been studied by Phi-value analysis. In combination with Phi-values from previous work, detailed insight into the transition states for folding of both yACBP and bACBP has been obtained. Of the 16 sequence positions that have been studied in both yACBP and bACBP, 5 (V12, I/L27, Y73, V77, and L80) have high Phi-values and appear to be important for the transition state formation in both homologues. Y31, A34, and A69 have high Phi-values only in yACBP, while F5, A9, and I74 have high Phi-values only in bACBP. Thus, additional interactions between helices A2 and A4 appear to be important for the transition state of yACBP, whereas additional interactions between helices A1 and A4 appear to be important for the transition state of bACBP. To examine whether these differences could be assigned to different packing of the residues in the native state, a solution structure of yACBP was determined by NMR. Small changes in the packing of the hydrophobic side-chains, which strengthen the interactions between helices A2 and A4, are observed in yACBP relative to bACBP. It is suggested that different structure elements serve as scaffolds for the folding of the 2 ACBP homologues.
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Affiliation(s)
- Kaare Teilum
- Institute of Molecular Biology, University of Copenhagen, Copenhagen, Denmark
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44
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Abstract
Seeding has been critical for obtaining diffraction-quality crystals for many structures. In this article, applications and recommendations for seeding are presented based on examples from our laboratory and other groups. The implementation of seeding in high-throughput crystallization, robotics, and other emerging technologies is also discussed.
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45
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Abstract
When a new protein structure has been determined, comparison with the database of known structures enables classification of its fold as new or belonging to a known class of proteins. This in turn may provide clues about the function of the protein. A large number of fold comparison programs have been developed, but they have never been subjected to a comprehensive and critical comparative analysis. Here we describe an evaluation of 11 publicly available, Web-based servers for automatic fold comparison. Both their functionality (e.g., user interface, presentation, and annotation of results) and their performance (i.e., how well established structural similarities are recognized) were assessed. The servers were subjected to a battery of performance tests covering a broad spectrum of folds as well as special cases, such as multidomain proteins, Calpha-only models, new folds, and NMR-based models. The CATH structural classification system was used as a reference. These tests revealed the strong and weak sides of each server. On the whole, CE, DALI, MATRAS, and VAST showed the best performance, but none of the servers achieved a 100% success rate. Where no structurally similar proteins are found by any individual server, it is recommended to try one or two other servers before any conclusions concerning the novelty of a fold are put on paper.
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Affiliation(s)
- Marian Novotny
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Uppsala, Sweden
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46
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He M, Burghardt TP, Vockley J. A novel approach to the characterization of substrate specificity in short/branched chain Acyl-CoA dehydrogenase. J Biol Chem 2003; 278:37974-86. [PMID: 12855692 DOI: 10.1074/jbc.m306882200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rat and human short/branched chain acyl-CoA dehydrogenases exhibit key differences in substrate specificity despite an overall amino acid identity of 85% between them. Rat short/branched chain acyl-CoA dehydrogenases (SBCAD) are more active toward substrates with longer carbon side chains than human SBCAD, whereas the human enzyme utilizes substrates with longer primary carbon chains. The mechanism underlying this difference in substrate specificity was investigated with a novel surface plasmon resonance assay combined with absorbance and circular dichroism spectroscopy, and kinetics analysis of wild type SBCADs and mutants with altered amino acid residues in the substrate binding pocket. Results show that a relatively few amino acid residues are critical for determining the difference in substrate specificity seen between the human and rat enzymes and that alteration of these residues influences different portions of the enzyme mechanism. Molecular modeling of the SBCAD structure suggests that position 104 at the bottom of the substrate binding pocket is important in determining the length of the primary carbon chain that can be accommodated. Conformational changes caused by alteration of residues at positions 105 and 177 directly affect the rate of electron transfer in the dehydrogenation reactions, and are likely transmitted from the bottom of the substrate binding pocket to beta-sheet 3. Differences between the rat and human enzyme at positions 383, 222, and 220 alter substrate specificity without affecting substrate binding. Modeling predicts that these residues combine to determine the distance between the flavin ring of FAD and the catalytic base, without changing the opening of the substrate binding pocket.
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Affiliation(s)
- Miao He
- Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota 55905, USA
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47
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Jakobsson E, Alvite G, Bergfors T, Esteves A, Kleywegt GJ. The crystal structure of Echinococcus granulosus fatty-acid-binding protein 1. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1649:40-50. [PMID: 12818189 DOI: 10.1016/s1570-9639(03)00151-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the 1.6 A crystal structure of the fatty-acid-binding protein EgFABP1 from the parasitic platyhelminth Echinococcus granulosus. E. granulosus causes hydatid disease, which is a major zoonosis. EgFABP1 has been implicated in the acquisition, storage, and transport of lipids, and may be important to the organism since it is incapable of synthesising most of its lipids de novo. Moreover, EgFABP1 is a promising candidate for a vaccine against hydatid disease. The crystal structure reveals that EgFABP1 has the expected 10-stranded beta-barrel fold typical of the family of intracellular lipid-binding proteins, and that it is structurally most similar to P2 myelin protein. We describe the comparison of the crystal structure of EgFABP1 with these proteins and with an older homology model for EgFABP1. The electron density reveals the presence of a bound ligand inside the cavity, which we have interpreted as palmitic acid. The carboxylate group of the fatty acid interacts with the protein's P2 motif, consisting of a conserved triad R em leader R-x-Y. The hydrophobic tail of the ligand assumes a fairly flat, U-shaped conformation and has relatively few interactions with the protein.We discuss some of the structural implications of the crystal structure of EgFABP1 for related platyhelminthic FABPs.
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Affiliation(s)
- Emma Jakobsson
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
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48
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Long chain acyl-CoA esters and acyl-CoA binding protein (ACBP) in cell function. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1569-2558(03)33008-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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49
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Cavagnari BM, Milikowski D, Haller JF, Zanek MC, Santomé JA, Ermácora MR. Optical characterization of armadillo acyl-CoA binding protein. Int J Biol Macromol 2002; 31:19-27. [PMID: 12559423 DOI: 10.1016/s0141-8130(02)00045-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Acyl-CoA binding protein (ACBP) and fatty acid binding protein (FABP) are intracellular transporters of activated and free fatty acids, respectively. Unlike other tissues with active lipid metabolism, armadillo Harderian gland contains much more ACBP than FABP. To characterize armadillo ACBP structure and binding properties, we produced it in Escherichia coli and carried out detailed fluorescence and circular dichroism spectroscopy studies. The K(D) for palmitoyl-CoA, measured directly by fluorescence and rotatory power, was 34+/-12 and 75+/-39 nM, respectively. The structure of armadillo ACBP appears to be very similar to that of bovine and rat liver ACBPs.
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Affiliation(s)
- Brian M Cavagnari
- Facultad de Farmacia y Bioquímica (UBA-CONICET), Instituto de Química y Fisicoquímica Biológicas, Juni;n 956, 1113, Buenos Aires, Argentina
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50
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van Aalten DM, DiRusso CC, Knudsen J. The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR. EMBO J 2001; 20:2041-50. [PMID: 11296236 PMCID: PMC125426 DOI: 10.1093/emboj/20.8.2041] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
FadR is an acyl-CoA-responsive transcription factor, regulating fatty acid biosynthetic and degradation genes in Escherichia coli. The apo-protein binds DNA as a homodimer, an interaction that is disrupted by binding of acyl-COA: The recently described structure of apo-FadR shows a DNA binding domain coupled to an acyl-CoA binding domain with a novel fold, but does not explain how binding of the acyl-CoA effector molecule > 30 A away from the DNA binding site affects transcriptional regulation. Here, we describe the structures of the FadR-operator and FadR- myristoyl-CoA binary complexes. The FadR-DNA complex reveals a novel winged helix-turn-helix protein-DNA interaction, involving sequence-specific contacts from the wing to the minor groove. Binding of acyl-CoA results in dramatic conformational changes throughout the protein, with backbone shifts up to 4.5 A. The net effect is a rearrangement of the DNA binding domains in the dimer, resulting in a change of 7.2 A in separation of the DNA recognition helices and the loss of DNA binding, revealing the molecular basis of acyl-CoA-responsive regulation.
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Affiliation(s)
- Daan M.F. van Aalten
- Wellcome Trust Biocentre, Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK,
The Center for Cardiovascular Sciences, Albany Medical College, Albany, NY, USA and Department of Biochemistry and Molecular Biology, Odense University, DK-5320 Odense M, Denmark Corresponding author e-mail:
| | - Concetta C. DiRusso
- Wellcome Trust Biocentre, Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK,
The Center for Cardiovascular Sciences, Albany Medical College, Albany, NY, USA and Department of Biochemistry and Molecular Biology, Odense University, DK-5320 Odense M, Denmark Corresponding author e-mail:
| | - Jens Knudsen
- Wellcome Trust Biocentre, Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK,
The Center for Cardiovascular Sciences, Albany Medical College, Albany, NY, USA and Department of Biochemistry and Molecular Biology, Odense University, DK-5320 Odense M, Denmark Corresponding author e-mail:
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