PyFuncover: full proteome search for a specific function using BLAST and PFAM

Python Function uncover (PyFuncover) is a new bioinformatic tool able to search proteins with a specific function in a full proteome. The pipeline coded in python uses BLAST alignment and the sequences from a PFAM family as the search seed. We tested PyFuncover using the fatty acid-binding family (FABP) Lipocalin_7 from PFAM (version 32, 2019) against the Homo sapiens NCBI proteome. After applying the scoring function in all the BLAST results, the data were classified and submitted to a GO-TERM analysis using bioDBnet. Analyses showed that all families of FABPs were ranked within the top scores. Included within this category were also families able to bind to hydrophobic molecules similar to fatty acids such as the retinol acid transporter and the cellular retinoic acid-binding protein.

Download Full-text

Rat intestinal fatty acid binding protein. A model system for analyzing the forces that can bind fatty acids to proteins.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)46634-8 ◽

1993 ◽

Vol 268 (25) ◽

pp. 18399-18402 ◽

Cited By ~ 2

Author(s):

J.C. Sacchettini ◽

J.I. Gordon

Keyword(s):

Fatty Acids ◽

Fatty Acid ◽

Fatty Acid Binding Protein ◽

Binding Protein ◽

Protein A ◽

Model System ◽

Fatty Acid Binding ◽

Acid Binding Protein

Download Full-text

Up-regulation of the expression of the gene for liver fatty acid-binding protein by long-chain fatty acids

Biochemical Journal ◽

10.1042/bj3190483 ◽

1996 ◽

Vol 319 (2) ◽

pp. 483-487 ◽

Cited By ~ 47

Author(s):

Claire MEUNIER-DURMORT ◽

Hélène POIRIER ◽

Isabelle NIOT ◽

Claude FOREST ◽

Philippe BESNARD

Keyword(s):

Fatty Acids ◽

Fatty Acid ◽

Fatty Acid Binding Protein ◽

Fold Increase ◽

Long Chain Fatty Acids ◽

Liver Fatty Acid ◽

Fatty Acid Binding ◽

Acid Binding Protein ◽

Fabp Gene ◽

Long Chain

The role of fatty acids in the expression of the gene for liver fatty acid-binding protein (L-FABP) was investigated in the well-differentiated FAO rat hepatoma cell line. Cells were maintained in serum-free medium containing 40 µM BSA/320 µM oleate. Western blot analysis showed that oleate triggered an approx. 4-fold increase in the cytosolic L-FABP level in 16 h. Oleate specifically stimulated L-FABP mRNA in time-dependent and dose-dependent manners with a maximum 7-fold increase at 16 h in FAO cells. Preincubation of FAO cells with cycloheximide prevented the oleate-mediated induction of L-FABP mRNA, showing that protein synthesis was required for the action of fatty acids. Run-on transcription assays demonstrated that the control of L-FABP gene expression by oleate was, at least in part, transcriptional. Palmitic acid, oleic acid, linoleic acid, linolenic acid and arachidonic acid were similarly potent whereas octanoic acid was inefficient. This regulation was also found in normal hepatocytes. Therefore long-chain fatty acids are strong inducers of L-FABP gene expression. FAO cells constitute a useful tool for studying the underlying mechanism of fatty acid action.

Download Full-text

The integrity of the α-helical domain of intestinal fatty acid binding protein is essential for the collision-mediated transfer of fatty acids to phospholipid membranes

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids ◽

10.1016/j.bbalip.2008.01.005 ◽

2008 ◽

Vol 1781 (4) ◽

pp. 192-199 ◽

Cited By ~ 15

Author(s):

G.R. Franchini ◽

J. Storch ◽

B. Corsico

Keyword(s):

Fatty Acids ◽

Fatty Acid ◽

Fatty Acid Binding Protein ◽

Binding Protein ◽

Phospholipid Membranes ◽

Fatty Acid Binding ◽

Acid Binding Protein ◽

Helical Domain

Download Full-text

Inhibition of binding to fatty acid binding protein reduces the intracellular transport of fatty acids

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.1996.271.1.g113 ◽

1996 ◽

Vol 271 (1) ◽

pp. G113-G120 ◽

Cited By ~ 4

Author(s):

B. A. Luxon

Keyword(s):

Fatty Acids ◽

Fatty Acid ◽

Intracellular Transport ◽

Fatty Acid Binding Protein ◽

Binding Protein ◽

Female Rats ◽

Dependent Manner ◽

Fatty Acid Binding ◽

Acid Binding Protein ◽

Cytoplasmic Transport

Male livers, containing lesser amounts of fatty acid binding protein (FABP), utilize fatty acids more slowly than female livers. Conventional wisdom dictates that FABP stimulates fatty acid use by increasing cytoplasmic transport rates. Previously, we showed that the cytoplasmic diffusion of a fatty acid analogue [12-N-methyl-7-nitrobenzo-2-oxa-1,3-diazol-amino stearate (NBD-stearate)] is faster in female hepatocytes, paralleling the larger amounts of FABP. Sex differences in other cytoplasmic factors could also lead to faster diffusion, independent of FABP levels. The aim of this study was to determine the effect of inhibition of fatty acid binding to FABP on the directly measured intracellular transport rate of NBD-stearate. The binding of NBD-stearate to FABP was reduced by incubating hepatocytes isolated from male and female rats with alpha-bromo-palmitate (0-1,500 microM), a modified long-chain fatty acid that binds to FABP. The inhibition by alpha-bromo-palmitate on NBD-stearate binding to FABP was measured with the use of centrifugation to separate cytosol from cytoplasmic membranes. Laser photobleaching (fluorescence recovery after photobleaching) was used to measure the cytoplasmic diffusion of NBD-stearate in hepatocytes. Alpha-Bromo-palmitate incubation reduced NBD-stearate binding to FABP in a dose-dependent manner. The measured diffusion rate was also reduced in proportion to the degree of binding inhibition. We conclude that cytoplasmic transport of NBD-stearate is modulated by binding to soluble proteins like FABP. FABP enhances diffusive transport by reducing binding to immobile cytosolic membranes.

Download Full-text