Trapping the dynamic acyl carrier protein in fatty acid biosynthesis

A highly specific chemical crosslinking method is used to trap a complex between an acyl carrier protein and a fatty acid dehydratase during fatty acid biosynthesis; subsequent X-ray crystallography, NMR spectroscopy and molecular dynamics simulations techniques enable the detailed study of this com...

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Veröffentlicht in:	Nature (London) Jg. 505; H. 7483; S. 427 - 431
Hauptverfasser:	Nguyen, Chi, Haushalter, Robert W., Lee, D. John, Markwick, Phineus R. L., Bruegger, Joel, Caldara-Festin, Grace, Finzel, Kara, Jackson, David R., Ishikawa, Fumihiro, O’Dowd, Bing, McCammon, J. Andrew, Opella, Stanley J., Tsai, Shiou-Chuan, Burkart, Michael D.
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	London Nature Publishing Group UK 16.01.2014 Nature Publishing Group
Schlagworte:	631/535/1266 631/92/287/1183 631/92/60 Acyl Carrier Protein - chemistry Acyl Carrier Protein - metabolism Binding Sites Biosynthesis Catalytic Domain Cross-Linking Reagents - chemistry Crosslinked polymers Crystal structure Crystallography, X-Ray Dehydration E coli Enzymes Escherichia coli - chemistry Fatty Acid Synthase, Type II - chemistry Fatty Acid Synthase, Type II - metabolism Fatty acids Fatty Acids - biosynthesis Histidine - metabolism Humanities and Social Sciences Hydro-Lyases - chemistry Hydro-Lyases - metabolism Infectious diseases letter Magnetic Resonance Spectroscopy Metabolites Models, Molecular Molecular Dynamics Simulation multidisciplinary NMR Nuclear magnetic resonance Physiological aspects Protein Binding Protein Interaction Maps Proteins Science Synthesis United States
ISSN:	0028-0836, 1476-4687, 1476-4687
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Abstract	A highly specific chemical crosslinking method is used to trap a complex between an acyl carrier protein and a fatty acid dehydratase during fatty acid biosynthesis; subsequent X-ray crystallography, NMR spectroscopy and molecular dynamics simulations techniques enable the detailed study of this complex. Acyl carrier protein structures revealed During fatty acid and polyketide biosynthesis the growing polymer chain is stabilized by acyl carrier proteins (ACPs), but the transient nature of the process makes it difficult to visualize the molecular mechanisms involved. Two papers published in this issue of Nature use strategies that circumvent this problem. Ali Masoudi et al . solve the X-ray crystal structures of an ACP from Escherichia coli bound to LpxD, an acyltransferase in the lipid A biosynthetic pathway, in three different states: an intact acyl-ACP, a hydrolysed-acyl-ACP, and a holo-ACP form. Alignment of these structures makes it possible to visualize the conformational changes that take place in the ACP during catalysis. Chi Nguyen et al . use a crosslinking probe to tether an ACP to an active site histidine of one of its catalytic enzymes, the dehydratase FabA from E. coli . They obtain a high-resolution X-ray crystal structure of the stabilized ACP–FabA complex and use NMR spectroscopy to probe the dynamics of ACP–FabA interactions. Their experiments support a 'switchblade' model. This crosslink-probe approach can be applied to other carrier protein partners in metabolic and signalling pathways. Acyl carrier protein (ACP) transports the growing fatty acid chain between enzymatic domains of fatty acid synthase (FAS) during biosynthesis 1 . Because FAS enzymes operate on ACP-bound acyl groups, ACP must stabilize and transport the growing lipid chain 2 . ACPs have a central role in transporting starting materials and intermediates throughout the fatty acid biosynthetic pathway 3 , 4 , 5 . The transient nature of ACP–enzyme interactions impose major obstacles to obtaining high-resolution structural information about fatty acid biosynthesis, and a new strategy is required to study protein–protein interactions effectively. Here we describe the application of a mechanism-based probe that allows active site-selective covalent crosslinking of AcpP to FabA, the Escherichia coli ACP and fatty acid 3-hydroxyacyl-ACP dehydratase, respectively. We report the 1.9 Å crystal structure of the crosslinked AcpP–FabA complex as a homodimer in which AcpP exhibits two different conformations, representing probable snapshots of ACP in action: the 4′-phosphopantetheine group of AcpP first binds an arginine-rich groove of FabA, then an AcpP helical conformational change locks AcpP and FabA in place. Residues at the interface of AcpP and FabA are identified and validated by solution nuclear magnetic resonance techniques, including chemical shift perturbations and residual dipolar coupling measurements. These not only support our interpretation of the crystal structures but also provide an animated view of ACP in action during fatty acid dehydration. These techniques, in combination with molecular dynamics simulations, show for the first time that FabA extrudes the sequestered acyl chain from the ACP binding pocket before dehydration by repositioning helix III. Extensive sequence conservation among carrier proteins suggests that the mechanistic insights gleaned from our studies may be broadly applicable to fatty acid, polyketide and non-ribosomal biosynthesis. Here the foundation is laid for defining the dynamic action of carrier-protein activity in primary and secondary metabolism, providing insight into pathways that can have major roles in the treatment of cancer, obesity and infectious disease.
AbstractList	Acyl carrier protein (ACP) transports the growing fatty acid chain between enzymatic domains of fatty acid synthase (FAS) during biosynthesis. Because FAS enzymes operate on ACP-bound acyl groups, ACP must stabilize and transport the growing lipid chain. ACPs have a central role in transporting starting materials and intermediates throughout the fatty acid biosynthetic pathway. The transient nature of ACP-enzyme interactions impose major obstacles to obtaining high-resolution structural information about fatty acid biosynthesis, and a new strategy is required to study protein-protein interactions effectively. Here we describe the application of a mechanism-based probe that allows active site-selective covalent crosslinking of AcpP to FabA, the Escherichia coli ACP and fatty acid 3-hydroxyacyl-ACP dehydratase, respectively. We report the 1.9 Å crystal structure of the crosslinked AcpP-FabA complex as a homodimer in which AcpP exhibits two different conformations, representing probable snapshots of ACP in action: the 4'-phosphopantetheine group of AcpP first binds an arginine-rich groove of FabA, then an AcpP helical conformational change locks AcpP and FabA in place. Residues at the interface of AcpP and FabA are identified and validated by solution nuclear magnetic resonance techniques, including chemical shift perturbations and residual dipolar coupling measurements. These not only support our interpretation of the crystal structures but also provide an animated view of ACP in action during fatty acid dehydration. These techniques, in combination with molecular dynamics simulations, show for the first time that FabA extrudes the sequestered acyl chain from the ACP binding pocket before dehydration by repositioning helix III. Extensive sequence conservation among carrier proteins suggests that the mechanistic insights gleaned from our studies may be broadly applicable to fatty acid, polyketide and non-ribosomal biosynthesis. Here the foundation is laid for defining the dynamic action of carrier-protein activity in primary and secondary metabolism, providing insight into pathways that can have major roles in the treatment of cancer, obesity and infectious disease. [PUBLICATION ABSTRACT] Acyl carrier protein (ACP) transports the growing fatty acid chain between enzyme domains of fatty acid synthase (FAS) during biosynthesis.1 Because FAS enzymes operate upon ACP-bound acyl groups, ACP must stabilize and transport the growing lipid chain.2 The transient nature of ACP-enzyme interactions imposes a major obstacle to gaining high-resolution structural information about fatty acid biosynthesis, and a new strategy is required to properly study protein-protein interactions. In this work, we describe the application of a mechanism-based probe that allows site-selective covalent crosslinking of AcpP to FabA, the E. coli ACP and fatty acid 3-hydroxyacyl-ACP dehydratase. We report the 1.9 Å crystal structure of the crosslinked AcpP=FabA complex as a homo-dimer, in which AcpP exhibits two different conformations likely representing snapshots of ACP in action: the 4′-phosphopantetheine (PPant) group of AcpP first binds an arginine-rich groove of FabA, followed by an AcpP helical conformational change that locks the AcpP and FabA in place. Residues at the interface of AcpP and FabA are identified and validated by solution NMR techniques, including chemical shift perturbations and RDC measurements. These not only support our interpretation of the crystal structures but also provide an animated view of ACP in action during fatty acid dehydration. Combined with molecular dynamics simulations, we show for the first time that FabA extrudes the sequestered acyl chain from the ACP binding pocket before dehydration by repositioning helix III. Extensive sequence conservation among carrier proteins suggests that the mechanistic insights gleaned from our studies will prove general for fatty acid, polyketide and non-ribosomal biosyntheses. Here the foundation is laid for defining the dynamic action of carrier protein activity in primary and secondary metabolism, providing insight into pathways that can play major roles in the treatment of cancer, obesity and infectious disease. Acyl carrier protein (ACP) transports the growing fatty acid chain between enzymatic domains of fatty acid synthase (FAS) during biosynthesis. Because FAS enzymes operate on ACP-bound acyl groups, ACP must stabilize and transport the growing lipid chain. ACPs have a central role in transporting starting materials and intermediates throughout the fatty acid biosynthetic pathway. The transient nature of ACP-enzyme interactions impose major obstacles to obtaining high-resolution structural information about fatty acid biosynthesis, and a new strategy is required to study protein-protein interactions effectively. Here we describe the application of a mechanism-based probe that allows active site-selective covalent crosslinking of AcpP to FabA, the Escherichia coli ACP and fatty acid 3-hydroxyacyl-ACP dehydratase, respectively. We report the 1.9 Å crystal structure of the crosslinked AcpP-FabA complex as a homodimer in which AcpP exhibits two different conformations, representing probable snapshots of ACP in action: the 4'-phosphopantetheine group of AcpP first binds an arginine-rich groove of FabA, then an AcpP helical conformational change locks AcpP and FabA in place. Residues at the interface of AcpP and FabA are identified and validated by solution nuclear magnetic resonance techniques, including chemical shift perturbations and residual dipolar coupling measurements. These not only support our interpretation of the crystal structures but also provide an animated view of ACP in action during fatty acid dehydration. These techniques, in combination with molecular dynamics simulations, show for the first time that FabA extrudes the sequestered acyl chain from the ACP binding pocket before dehydration by repositioning helix III. Extensive sequence conservation among carrier proteins suggests that the mechanistic insights gleaned from our studies may be broadly applicable to fatty acid, polyketide and non-ribosomal biosynthesis. Here the foundation is laid for defining the dynamic action of carrier-protein activity in primary and secondary metabolism, providing insight into pathways that can have major roles in the treatment of cancer, obesity and infectious disease.Acyl carrier protein (ACP) transports the growing fatty acid chain between enzymatic domains of fatty acid synthase (FAS) during biosynthesis. Because FAS enzymes operate on ACP-bound acyl groups, ACP must stabilize and transport the growing lipid chain. ACPs have a central role in transporting starting materials and intermediates throughout the fatty acid biosynthetic pathway. The transient nature of ACP-enzyme interactions impose major obstacles to obtaining high-resolution structural information about fatty acid biosynthesis, and a new strategy is required to study protein-protein interactions effectively. Here we describe the application of a mechanism-based probe that allows active site-selective covalent crosslinking of AcpP to FabA, the Escherichia coli ACP and fatty acid 3-hydroxyacyl-ACP dehydratase, respectively. We report the 1.9 Å crystal structure of the crosslinked AcpP-FabA complex as a homodimer in which AcpP exhibits two different conformations, representing probable snapshots of ACP in action: the 4'-phosphopantetheine group of AcpP first binds an arginine-rich groove of FabA, then an AcpP helical conformational change locks AcpP and FabA in place. Residues at the interface of AcpP and FabA are identified and validated by solution nuclear magnetic resonance techniques, including chemical shift perturbations and residual dipolar coupling measurements. These not only support our interpretation of the crystal structures but also provide an animated view of ACP in action during fatty acid dehydration. These techniques, in combination with molecular dynamics simulations, show for the first time that FabA extrudes the sequestered acyl chain from the ACP binding pocket before dehydration by repositioning helix III. Extensive sequence conservation among carrier proteins suggests that the mechanistic insights gleaned from our studies may be broadly applicable to fatty acid, polyketide and non-ribosomal biosynthesis. Here the foundation is laid for defining the dynamic action of carrier-protein activity in primary and secondary metabolism, providing insight into pathways that can have major roles in the treatment of cancer, obesity and infectious disease. Acyl carrier protein (ACP) transports the growing fatty acid chain between enzymatic domains of fatty acid synthase (FAS) during biosynthesis. Because FAS enzymes operate on ACP-bound acyl groups, ACP must stabilize and transport the growing lipid chain. ACPs have a central role in transporting starting materials and intermediates throughout the fatty acid biosynthetic pathway. The transient nature of ACP-enzyme interactions impose major obstacles to obtaining high-resolution structural information about fatty acid biosynthesis, and a new strategy is required to study protein-protein interactions effectively. Here we describe the application of a mechanism-based probe that allows active site-selective covalent crosslinking of AcpP to FabA, the Escherichia coli ACP and fatty acid 3-hydroxyacyl-ACP dehydratase, respectively. We report the 1.9 Å crystal structure of the crosslinked AcpP-FabA complex as a homodimer in which AcpP exhibits two different conformations, representing probable snapshots of ACP in action: the 4'-phosphopantetheine group of AcpP first binds an arginine-rich groove of FabA, then an AcpP helical conformational change locks AcpP and FabA in place. Residues at the interface of AcpP and FabA are identified and validated by solution nuclear magnetic resonance techniques, including chemical shift perturbations and residual dipolar coupling measurements. These not only support our interpretation of the crystal structures but also provide an animated view of ACP in action during fatty acid dehydration. These techniques, in combination with molecular dynamics simulations, show for the first time that FabA extrudes the sequestered acyl chain from the ACP binding pocket before dehydration by repositioning helix III. Extensive sequence conservation among carrier proteins suggests that the mechanistic insights gleaned from our studies may be broadly applicable to fatty acid, polyketide and non-ribosomal biosynthesis. Here the foundation is laid for defining the dynamic action of carrier-protein activity in primary and secondary metabolism, providing insight into pathways that can have major roles in the treatment of cancer, obesity and infectious disease. Acyl carrier protein (ACP) transports the growing fatty acid chain between enzymatic domains of fatty acid synthase (FAS) during biosynthesis (1). Because FAS enzymes operate on ACP-bound acyl groups, ACP must stabilize and transport the growing lipid chain (2). ACPs have a central role in transporting starting materials and intermediates throughout the fatty acid biosynthetic pathway (3-5). The transient nature of ACP-enzyme interactions impose major obstacles to obtaining high-resolution structural information about fatty acid biosynthesis, and a new strategy is required to study protein-protein interactions effectively. Here we describe the application of a mechanism-based probe that allows active site-selective covalent crosslinking of AcpP to FabA, the Escherichia coli ACP and fatty acid 3-hydroxyacyl-ACP dehydratase, respectively. We report the 1.9 Å crystal structure of the crosslinked AcpP-FabA complex as a homodimer in which AcpP exhibits two different conformations, representing probable snapshots of ACP in action: the 4'-phosphopantetheine group of AcpP first binds an arginine-rich groove of FabA, then an AcpP helical conformational change locks AcpP and FabA in place. Residues at the interface of AcpP and FabA are identified and validated by solution nuclear magnetic resonance techniques, including chemical shift perturbations and residual dipolar coupling measurements. These not only support our interpretation of the crystal structures but also provide an animated view of ACP in action during fatty acid dehydration. These techniques, in combination with molecular dynamics simulations, show for the first time that FabA extrudes the sequestered acyl chain from the ACP binding pocket before dehydration by repositioning helix III. Extensive sequence conservation among carrier proteins suggests that the mechanistic insights gleaned from our studies may be broadly applicable to fatty acid, polyketide and non-ribosomal biosynthesis. Here the foundation is laid for defining the dynamic action of carrier-protein activity in primary and secondary metabolism, providing insight into pathways that can have major roles in the treatment of cancer, obesity and infectious disease. A highly specific chemical crosslinking method is used to trap a complex between an acyl carrier protein and a fatty acid dehydratase during fatty acid biosynthesis; subsequent X-ray crystallography, NMR spectroscopy and molecular dynamics simulations techniques enable the detailed study of this complex. Acyl carrier protein structures revealed During fatty acid and polyketide biosynthesis the growing polymer chain is stabilized by acyl carrier proteins (ACPs), but the transient nature of the process makes it difficult to visualize the molecular mechanisms involved. Two papers published in this issue of Nature use strategies that circumvent this problem. Ali Masoudi et al . solve the X-ray crystal structures of an ACP from Escherichia coli bound to LpxD, an acyltransferase in the lipid A biosynthetic pathway, in three different states: an intact acyl-ACP, a hydrolysed-acyl-ACP, and a holo-ACP form. Alignment of these structures makes it possible to visualize the conformational changes that take place in the ACP during catalysis. Chi Nguyen et al . use a crosslinking probe to tether an ACP to an active site histidine of one of its catalytic enzymes, the dehydratase FabA from E. coli . They obtain a high-resolution X-ray crystal structure of the stabilized ACP–FabA complex and use NMR spectroscopy to probe the dynamics of ACP–FabA interactions. Their experiments support a 'switchblade' model. This crosslink-probe approach can be applied to other carrier protein partners in metabolic and signalling pathways. Acyl carrier protein (ACP) transports the growing fatty acid chain between enzymatic domains of fatty acid synthase (FAS) during biosynthesis 1 . Because FAS enzymes operate on ACP-bound acyl groups, ACP must stabilize and transport the growing lipid chain 2 . ACPs have a central role in transporting starting materials and intermediates throughout the fatty acid biosynthetic pathway 3 , 4 , 5 . The transient nature of ACP–enzyme interactions impose major obstacles to obtaining high-resolution structural information about fatty acid biosynthesis, and a new strategy is required to study protein–protein interactions effectively. Here we describe the application of a mechanism-based probe that allows active site-selective covalent crosslinking of AcpP to FabA, the Escherichia coli ACP and fatty acid 3-hydroxyacyl-ACP dehydratase, respectively. We report the 1.9 Å crystal structure of the crosslinked AcpP–FabA complex as a homodimer in which AcpP exhibits two different conformations, representing probable snapshots of ACP in action: the 4′-phosphopantetheine group of AcpP first binds an arginine-rich groove of FabA, then an AcpP helical conformational change locks AcpP and FabA in place. Residues at the interface of AcpP and FabA are identified and validated by solution nuclear magnetic resonance techniques, including chemical shift perturbations and residual dipolar coupling measurements. These not only support our interpretation of the crystal structures but also provide an animated view of ACP in action during fatty acid dehydration. These techniques, in combination with molecular dynamics simulations, show for the first time that FabA extrudes the sequestered acyl chain from the ACP binding pocket before dehydration by repositioning helix III. Extensive sequence conservation among carrier proteins suggests that the mechanistic insights gleaned from our studies may be broadly applicable to fatty acid, polyketide and non-ribosomal biosynthesis. Here the foundation is laid for defining the dynamic action of carrier-protein activity in primary and secondary metabolism, providing insight into pathways that can have major roles in the treatment of cancer, obesity and infectious disease.
Audience	Academic
Author	Tsai, Shiou-Chuan Ishikawa, Fumihiro Lee, D. John Burkart, Michael D. Markwick, Phineus R. L. McCammon, J. Andrew Opella, Stanley J. Finzel, Kara Jackson, David R. Bruegger, Joel O’Dowd, Bing Haushalter, Robert W. Caldara-Festin, Grace Nguyen, Chi
AuthorAffiliation	3 San Diego Supercomputer Center 1 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 2 Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, CA 92697 4 Howard Hughes Medical Institute, La Jolla, CA 92093
AuthorAffiliation_xml	– name: 4 Howard Hughes Medical Institute, La Jolla, CA 92093 – name: 1 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 – name: 3 San Diego Supercomputer Center – name: 2 Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, CA 92697
Author_xml	– sequence: 1 givenname: Chi surname: Nguyen fullname: Nguyen, Chi organization: Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California – sequence: 2 givenname: Robert W. surname: Haushalter fullname: Haushalter, Robert W. organization: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA – sequence: 3 givenname: D. John surname: Lee fullname: Lee, D. John organization: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA – sequence: 4 givenname: Phineus R. L. surname: Markwick fullname: Markwick, Phineus R. L. organization: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA, San Diego Supercomputer Center, Howard Hughes Medical Institute – sequence: 5 givenname: Joel surname: Bruegger fullname: Bruegger, Joel organization: Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California – sequence: 6 givenname: Grace surname: Caldara-Festin fullname: Caldara-Festin, Grace organization: Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California – sequence: 7 givenname: Kara surname: Finzel fullname: Finzel, Kara organization: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA – sequence: 8 givenname: David R. surname: Jackson fullname: Jackson, David R. organization: Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California – sequence: 9 givenname: Fumihiro surname: Ishikawa fullname: Ishikawa, Fumihiro organization: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA – sequence: 10 givenname: Bing surname: O’Dowd fullname: O’Dowd, Bing organization: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA – sequence: 11 givenname: J. Andrew surname: McCammon fullname: McCammon, J. Andrew organization: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA, Howard Hughes Medical Institute – sequence: 12 givenname: Stanley J. surname: Opella fullname: Opella, Stanley J. organization: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA – sequence: 13 givenname: Shiou-Chuan surname: Tsai fullname: Tsai, Shiou-Chuan email: sctsai@uci.edu organization: Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California – sequence: 14 givenname: Michael D. surname: Burkart fullname: Burkart, Michael D. email: mburkart@ucsd.edu organization: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/24362570$$D View this record in MEDLINE/PubMed
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Snippet	A highly specific chemical crosslinking method is used to trap a complex between an acyl carrier protein and a fatty acid dehydratase during fatty acid... Acyl carrier protein (ACP) transports the growing fatty acid chain between enzymatic domains of fatty acid synthase (FAS) during biosynthesis. Because FAS... Acyl carrier protein (ACP) transports the growing fatty acid chain between enzymatic domains of fatty acid synthase (FAS) during biosynthesis (1). Because FAS... Acyl carrier protein (ACP) transports the growing fatty acid chain between enzyme domains of fatty acid synthase (FAS) during biosynthesis.1 Because FAS...
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SubjectTerms	631/535/1266 631/92/287/1183 631/92/60 Acyl Carrier Protein - chemistry Acyl Carrier Protein - metabolism Binding Sites Biosynthesis Catalytic Domain Cross-Linking Reagents - chemistry Crosslinked polymers Crystal structure Crystallography, X-Ray Dehydration E coli Enzymes Escherichia coli - chemistry Fatty Acid Synthase, Type II - chemistry Fatty Acid Synthase, Type II - metabolism Fatty acids Fatty Acids - biosynthesis Histidine - metabolism Humanities and Social Sciences Hydro-Lyases - chemistry Hydro-Lyases - metabolism Infectious diseases letter Magnetic Resonance Spectroscopy Metabolites Models, Molecular Molecular Dynamics Simulation multidisciplinary NMR Nuclear magnetic resonance Physiological aspects Protein Binding Protein Interaction Maps Proteins Science Synthesis
Title	Trapping the dynamic acyl carrier protein in fatty acid biosynthesis
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