Dynamic Mechanism of Fatty Acid Transport across Cellular Membranes through FadL: Molecular Dynamics Simulations

2008 ◽  
Vol 112 (41) ◽  
pp. 13070-13078 ◽  
Author(s):  
Hanjun Zou ◽  
Mingyue Zheng ◽  
Xiaomin Luo ◽  
Weiliang Zhu ◽  
Kaixian Chen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Fatty Acid ◽  
Molecular Dynamics Simulations ◽  
Dynamic Mechanism ◽  
Fatty Acid Transport ◽  
Acid Transport ◽  
Cellular Membranes ◽  
Dynamics Simulations

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.

Molecular mechanism with regard to the binding selectivity of inhibitors toward FABP5 and FABP7 explored by multiple short molecular dynamics simulations and free energy analyses

2020 ◽  
Vol 22 (4) ◽  
pp. 2262-2275 ◽  
Author(s):  
Jianzhong Chen ◽  
Xinguo Liu ◽  
Shaolong Zhang ◽  
Junxiao Chen ◽  
Haibo Sun ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Fatty Acid ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanism ◽  
Binding Proteins ◽  
Fatty Acid Binding Proteins ◽  
Binding Selectivity ◽  
Fatty Acid Binding ◽  
Dynamics Simulations

Recently, fatty acid binding proteins 5 and 7 (FABP5 and FABP7) have been regarded as the prospective targets for clinically treating multiple diseases related to FABPs.

Dynamic Mechanism for the Autophosphorylation of CheA Histidine Kinase:  Molecular Dynamics Simulations

2005 ◽  
Vol 127 (33) ◽  
pp. 11709-11719 ◽  
Author(s):  
Jian Zhang ◽  
Yechun Xu ◽  
Jianhua Shen ◽  
Xiaomin Luo ◽  
Jiagao Chen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Histidine Kinase ◽  
Dynamic Mechanism ◽  
Dynamics Simulations

Tight knots in proteins: can they block the mitochondrial pores?

2013 ◽  
Vol 41 (2) ◽  
pp. 620-624 ◽  
Author(s):  
Piotr Szymczak
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Present Article ◽  
Protein Translocation ◽  
Cellular Membranes ◽  
Numerical Studies ◽  
Knotted Protein ◽  
Knotted Proteins ◽  
Dynamics Simulations

Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process since the diameter of the pore is smaller than the size of maximally tightened knot. In the present article, I briefly review the experimental and numerical studies of tight knots in proteins, with a particular emphasis on the estimates of the size of these knots. Next, I discuss the process of protein translocation through the mitochondrial pores and report the results of molecular dynamics simulations of knotted protein translocation, which show how the knot can indeed block the pore.

scholarly journals Fast Vesicle Fusion Mediated by Hydrophobic Dipeptides

2020 ◽  
Author(s):  
C. Wei ◽  
A. Pohorille
Keyword(s):  
Molecular Dynamics ◽  
Fatty Acid ◽  
Molecular Dynamics Simulations ◽  
Membrane Surface ◽  
Vesicle Fusion ◽  
Side Chains ◽  
Preferential Growth ◽  
Evolutionary Advantage ◽  
Inanimate Matter ◽  
Dynamics Simulations

AbstractTo understand the transition from inanimate matter to life, we studied a process that directly couples simple metabolism to evolution via natural selection, demonstrated experimentally by Adamala and Szostak (Nat. Chem. 2013, 5, 495–501). In this process, dipeptides synthesized inside precursors of cells promote absorption of fatty acid micelles to vesicles inducing their preferential growth and division at the expense of other vesicles. The process is explained on the basis of coarse-grained molecular dynamics simulations, each extending for tens of microseconds, carried out to model fusion between a micelle and a membrane, both made of fatty acids in the absence and presence of hydrophobic dipeptides. In all systems with dipeptides, but not in their absence, fusion events were observed. They involve the formation of a stalk made by hydrophobic chains from the micelle and the membrane, similar to that postulated for vesicle-vesicle fusion. The emergence of a stalk is facilitated by transient clusters of dipeptides, side chains of which formed hydrophobic patches at the membrane surface. Committor probability calculations indicate that the size of a patch is a suitable reaction coordinate and allow for identifying the transition state for fusion. Free energy barrier to fusion is greatly reduced in the presence of dipeptides to only 4-5 kcal/mol, depending of the hydrophobicity of side chains. The mechanism of mediated fusion, which is expected to apply to other small peptides and hydrophobic molecules, provides a robust means by which a nascent metabolism can confer evolutionary advantage to precursors of cells.SignificanceWe study fusion of micelles and vesicles in the presence and absence of hydrophobic dipeptides by way of molecular dynamics simulations and demonstrate the spontaneous formation of a hydrophobic stalk that has been also long postulated as the key process in vesicle-vesicle fusion but shown only in forced simulations. We show that fusion is facilitated by clusters of dipeptides that form hydrophobic patches at the membrane surface. In order to understand the transition from inanimate matter to life, we explain and generalize experimental findings that hydrophobic dipeptides synthesized inside precursors of cells promote absorption of fatty acid micelles to vesicles inducing their preferential growth and division, thus providing cells endowed with such metabolism with evolutionary advantage.

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