Molecular dynamics simulations of the auxin-binding protein 1 in complex with indole-3-acetic acid and naphthalen-1-acetic acid

2014 ◽  
Vol 82 (10) ◽  
pp. 2744-2755 ◽  
Author(s):  
Melanie Grandits ◽  
Chris Oostenbrink
Keyword(s):  
Molecular Dynamics ◽  
Acetic Acid ◽  
Molecular Dynamics Simulations ◽  
Binding Protein ◽  
Auxin Binding ◽  
Dynamics Simulations ◽  
Auxin Binding Protein ◽  
Indole 3 Acetic Acid

An Auxin Binding Protein is Localized in the Symbiosome Membrane of Soybean Nodules

1993 ◽  
Vol 48 (1-2) ◽  
pp. 35-40 ◽  
Author(s):  
Andreas Jacobi ◽  
Rolf Zettl ◽  
Klaus Palme ◽  
Dietrich Werner
Keyword(s):  
Acetic Acid ◽  
Auxin Transport ◽  
Binding Protein ◽  
Naphthaleneacetic Acid ◽  
Dependent Manner ◽  
Symbiosome Membrane ◽  
Auxin Binding ◽  
Auxin Binding Protein ◽  
Triton X ◽  
Indole 3 Acetic Acid

Binding of tritiated indole-3-acetic acid ([3H]IAA) to symbiosome membranes of soybean nodules occurred in a protein-dependent manner and was competitively inhibited by unlabeled indole-3-acetic acid (IAA), 1-naphthaleneacetic acid (1-NAA) and dithiothreitol (DTT), but not by tryptophan and benzoic acid. The symbiosome membranes bound IAA with a KD of 1 × 10-6 m. Photoaffinity labeling identified an auxin-binding protein (ABP) in the symbiosome membrane with an apparent molecular mass of 23 kDa. This 23 kDa protein was labeled either with 5-azido-[7-3H]indole-3-acetic acid ([3H]N3IAA) or with 5′-azido-[3,6-3H2]-1-naphthylphthalamic acid ([3H2]N3NPA). Labeling of the 23 kDa protein with [3H]N3IAA was competitively inhibited by unlabeled IAA and 1-NAA. NPA and quercetin, inhibitors of polar auxin transport, as well as rutin, a glycosylated derivative of quercetin, competed with IAA for binding. Conversely, [3H2]N3NPA labeling was inhibited by unlabeled IAA and NPA. The 23 kDa symbiosome membrane protein was partially solubilized with Triton X-100 and nearly completely using Triton X-114. The observation that auxin transport inhibitors compete with IAA for binding suggests that the symbiosome membrane ABP could be part of an auxin efflux carrier system required to control the auxin concentration in infected soybean nodule cells.

Molecular dynamics simulations of palmitate entry into the hydrophobic pocket of the fatty acid binding protein

FEBS Letters ◽  
2007 ◽  
Vol 581 (6) ◽  
pp. 1243-1247 ◽  
Author(s):  
Yossi Tsfadia ◽  
Ran Friedman ◽  
Jonathan Kadmon ◽  
Anna Selzer ◽  
Esther Nachliel ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Fatty Acid ◽  
Molecular Dynamics Simulations ◽  
Fatty Acid Binding Protein ◽  
Binding Protein ◽  
Hydrophobic Pocket ◽  
Fatty Acid Binding ◽  
Acid Binding Protein ◽  
Dynamics Simulations

scholarly journals Brain fatty acid binding protein exhibits non-preferential and mutation-resistant binding towards fatty acids

2021 ◽  
Author(s):  
Iulia Bodnariuc ◽  
Stefan Lenz ◽  
Margaret Renaud-Young ◽  
Tanille Shandro ◽  
Hiroaki Ishida ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Fatty Acids ◽  
Fatty Acid ◽  
Molecular Dynamics Simulations ◽  
Nuclear Localization ◽  
Fatty Acid Binding Protein ◽  
Binding Protein ◽  
Fatty Acid Binding ◽  
Acid Binding Protein ◽  
Dynamics Simulations

Members of the fatty acid binding protein (FABP) family function as intracellular transporters of long chain fatty acids and other hydrophobic molecules to different cellular compartments. Brain fatty acid binding protein (FABP7) exhibits ligand-directed differences in cellular transport behavior. For example, when FABP7 binds to docosahexaenoic acid (DHA), the complex relocates to the nucleus and influences transcriptional activity, whereas FABP7 bound with monosaturated fatty acids remain in the cytosol. We used a variety of biophysical techniques to enhance understanding of ligand-directed transport. Specifically, we examine how FABP7 binds to fatty acids, including saturated stearic acid (SA), monounsaturated oleic acid (OA), and polyunsaturated DHA. We find that at 37°C FABP7 has near equivalent binding affinities for the fatty acids, while at lower temperatures, FABP7 exhibits a preference for the unsaturated fatty acids. Therefore, nuclear localization of the FABP7-DHA complex cannot be explained by binding preferences. Using NMR spectroscopy and molecular dynamics simulations, we observe that DHA uniquely affects the portal region of FABP7, which could enhance the complex's nuclear localization. Mutations to purported critical binding residues (R126L and Y128F) have little effect on fatty acid binding, with molecular dynamics simulations revealing that the bound fatty acid can adopt binding poses that can accommodate the mutations.

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