scholarly journals MBPpred: Proteome-wide detection of membrane lipid-binding proteins using profile Hidden Markov Models

2015 ◽  
Author(s):  
Katerina C. Nastou ◽  
Georgios N. Tsaousis ◽  
Nikolaos C. Papandreou ◽  
Stavros J. Hamodrakas
Keyword(s):  
Binding Proteins ◽  
Markov Models ◽  
Membrane Lipids ◽  
Hidden Markov ◽  
Membrane Binding ◽  
Membrane Lipid ◽  
Lipid Binding ◽  
Binding Domains ◽  
Eukaryotic Proteomes ◽  
Lipid Binding Proteins

ABSTRACTA large number of modular domains that exhibit specific lipid binding properties are present in many membrane proteins involved in trafficking and signal transduction. These domains are present in either eukaryotic peripheral membrane or transmembrane proteins and are responsible for the non-covalent interactions of these proteins with membrane lipids. Here we report a profile Hidden Markov Model based method capable of detecting Membrane Binding Proteins (MBPs) from information encoded in their amino acid sequence, called MBPpred. The method identifies MBPs that contain one or more of the Membrane Binding Domains (MBDs) that have been described to date, and further classifies these proteins based on their position in respect to the membrane, either as peripheral or transmembrane. MBPpred is available online at http://bioinformatics.biol.uoa.gr/MBPpred. This method was applied in selected eukaryotic proteomes, in order to examine the characteristics they exhibit in various eukaryotic kingdoms and phylums.

scholarly journals MCE domain proteins: conserved inner membrane lipid-binding proteins required for outer membrane homeostasis

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Georgia L. Isom ◽  
Nathaniel J. Davies ◽  
Zhi-Soon Chong ◽  
Jack A. Bryant ◽  
Mohammed Jamshad ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Binding Proteins ◽  
Membrane Lipid ◽  
Lipid Binding ◽  
Inner Membrane ◽  
Lipid Binding Proteins

The role of dynamics in modulating ligand exchange in intracellular lipid binding proteins

2014 ◽  
Vol 1844 (7) ◽  
pp. 1268-1278 ◽  
Author(s):  
Laura Ragona ◽  
Katiuscia Pagano ◽  
Simona Tomaselli ◽  
Filippo Favretto ◽  
Alberto Ceccon ◽  
...  
Keyword(s):  
Ligand Exchange ◽  
Binding Proteins ◽  
Lipid Binding ◽  
Intracellular Lipid ◽  
Lipid Binding Proteins

scholarly journals INTRACELLULAR LIPID-BINDING PROTEINS AND THEIR GENES

1997 ◽  
Vol 17 (1) ◽  
pp. 277-303 ◽  
Author(s):  
David A. Bernlohr ◽  
Melanie A. Simpson ◽  
Ann Vogel Hertzel ◽  
Leonard J. Banaszak
Keyword(s):  
Binding Proteins ◽  
Lipid Binding ◽  
Intracellular Lipid ◽  
Lipid Binding Proteins

Abstract 583: Characterization of Cell Membrane Microdomains Facilitating HDL Biogenesis

2014 ◽  
Vol 34 (suppl_1) ◽  
Author(s):  
Hong Choi ◽  
Isabelle Ruel ◽  
Rui Hao Leo Wang ◽  
Jacques Genest
Keyword(s):  
Cell Membrane ◽  
Cell Surface ◽  
Protease Inhibitors ◽  
Binding Proteins ◽  
Lipid Binding ◽  
Cholesterol Homeostasis ◽  
Scaffolding Protein ◽  
Membrane Microdomains ◽  
Discontinuous Sucrose Gradient ◽  
Lipid Binding Proteins

High-density lipoprotein (HDL) particles, generated in the process of removing excess cellular cholesterol, play crucial roles in maintaining cholesterol homeostasis in arterial cells and in protecting the cardiovascular system from the development of atherosclerosis. Cholesterol-loaded cells increase their binding capacity to the HDL scaffolding protein, apolipoprotein A-I (ApoA-I), however, cell surface factors necessary for ApoA-I binding remains to be elucidated. To characterize cell membrane microdomains interacting with ApoA-I, primary human skin fibroblasts were incubated with ApoA-I for 1h at 4°C. After linking protein-protein interactions with a membrane-impermeable crosslinker, DTSSP, cells were subjected to homogenization. The cell homogenate was separated by a discontinuous sucrose gradient centrifugation and ten fractions were collected. ApoA-I-associated cell membrane fraction was located by immunoblotting for ApoA-I and organelle markers. Membrane-containing fractions were fragmented using sonication prior to immunoprecipitation of ApoA-I-associated microdomains using an anti-ApoA-I antibody. Major lipid classes present in the microdomains are phosphatidylcholine, phosphatidylserine, sphingomyelin and cholesterol. Two cell membrane proteins, caveolin and ABCA1, were excluded from the microdomains. These data suggest that ApoA-I bind to cholesterol-rich cell surface microdomains that are different from ABCA1 and caveolae domains. LC-MS/MS analysis identified the presence of 26 proteins in the microdomains. Among these, several desmosomal proteins, lipid binding proteins and protease inhibitors were identified. Overall, our results suggest that the initial binding of ApoA-I to cell surface occurs on the lateral sides of cell membranes where desmosomal proteins provide a binding site for ApoA-I, and that lipid binding proteins facilitate lipidation of ApoA-I while protease inhibitors protect ApoA-I and related proteins from degradation. In conclusion, we established a new method to isolate cell membrane microdomains interacting with ApoA-I. Using this method, we found that ApoA-I associates with desmosomal proteins for the formation of HDL.

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