scholarly journals Lipid-protein interaction induced domains: Kinetics and conformational changes in multicomponent vesicles

2018 ◽  
Vol 148 (13) ◽  
pp. 134703 ◽  
Author(s):  
K. K. Sreeja ◽  
P. B. Sunil Kumar
Keyword(s):  
Conformational Changes ◽  
Protein Interaction ◽  
Lipid Protein Interaction

Preparation of Chloroplast Lipid Membrane and Lipid-protein Interaction Assay

BIO-PROTOCOL ◽  
2016 ◽  
Vol 6 (3) ◽  
Author(s):  
Kumiko Okazaki ◽  
Shin-ya Miyagishima ◽  
Hajime Wada
Keyword(s):  
Protein Interaction ◽  
Lipid Membrane ◽  
Lipid Protein Interaction

Effect of lipid-protein interaction on the color of bacteriorhodopsin

1989 ◽  
Vol 973 (2) ◽  
pp. 257-262 ◽  
Author(s):  
C. Pande ◽  
R. Callender ◽  
J. Baribeau ◽  
F. Boucher ◽  
A. Pande
Keyword(s):  
Protein Interaction ◽  
Lipid Protein Interaction

scholarly journals Simplified geometric representations of protein structures identify complementary interaction interfaces

2019 ◽  
Author(s):  
Caitlyn L. McCafferty ◽  
Edward M. Marcotte ◽  
David W. Taylor
Keyword(s):  
Conformational Changes ◽  
Protein Interaction ◽  
Protein Function ◽  
Large Scale ◽  
Predictive Accuracy ◽  
Protein Complexes ◽  
Protein Structures ◽  
Molecular Properties ◽  
3D Structures ◽  
Geometric Representations

ABSTRACTProtein-protein interactions are critical to protein function, but three-dimensional (3D) arrangements of interacting proteins have proven hard to predict, even given the identities and 3D structures of the interacting partners. Specifically, identifying the relevant pairwise interaction surfaces remains difficult, often relying on shape complementarity with molecular docking while accounting for molecular motions to optimize rigid 3D translations and rotations. However, such approaches can be computationally expensive, and faster, less accurate approximations may prove useful for large-scale prediction and assembly of 3D structures of multi-protein complexes. We asked if a reduced representation of protein geometry retains enough information about molecular properties to predict pairwise protein interaction interfaces that are tolerant of limited structural rearrangements. Here, we describe a cuboid transformation of 3D protein accessible surfaces on which molecular properties such as charge, hydrophobicity, and mutation rate can be easily mapped, implemented in the MorphProt package. Pairs of surfaces are compared to rapidly assess partner-specific potential surface complementarity. On two available benchmarks of 85 overall known protein complexes, we observed F1 scores (a weighted combination of precision and recall) of 19-34% at correctly identifying protein interaction surfaces, comparable to more computationally intensive 3D docking methods in the annual Critical Assessment of PRedicted Interactions. Furthermore, we examined the effect of molecular motion through normal mode simulation on a benchmark receptor-ligand pair and observed no marked loss of predictive accuracy for distortions of up to 6 Å RMSD. Thus, a cuboid transformation of protein surfaces retains considerable information about surface complementarity, offers enhanced speed of comparison relative to more complex geometric representations, and exhibits tolerance to conformational changes.

The influence of the lipid–protein interaction on the membrane dynamics

2004 ◽  
Vol 350 (1-3) ◽  
pp. E623-E626 ◽  
Author(s):  
F Natali ◽  
A Relini ◽  
A Gliozzi ◽  
R Rolandi ◽  
P Cavatorta ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Membrane Dynamics ◽  
Lipid Protein Interaction

Arachidonic acid and its metabolites increase Cai in cultured rat oligodendrocytes

1993 ◽  
Vol 264 (3) ◽  
pp. C632-C640 ◽  
Author(s):  
B. Soliven ◽  
M. Takeda ◽  
T. Shandy ◽  
D. J. Nelson
Keyword(s):  
Spinal Cord ◽  
Arachidonic Acid ◽  
Linoleic Acid ◽  
Intracellular Calcium ◽  
Protein Interaction ◽  
Membrane Lipid ◽  
Rat Spinal Cord ◽  
Fura 2 ◽  
Fluorescence Measurements ◽  
Lipid Protein Interaction

Fluorescence measurements of intracellular calcium (Cai) were made on cultured rat spinal cord oligodendrocytes (OLGs) using the dye fura-2. Exposure of OLGs to arachidonic acid (AA) (5-50 microM) elicited a concentration-dependent increase in Cai that was derived mainly from extracellular Ca2+. AA at 50 microM also released Ca2+ from intracellular stores. The response to AA was not decreased by nifedipine or by inhibition of Na(+)-Ca2+ exchange. AA-induced Ca2+ influx pathway was permeable to Mn2+ and Co2+ but not to Ba2+ and was not markedly influenced by depolarization, suggesting that AA activates a voltage-independent, not strictly selective, Ca2+ channel. The Cai response to AA was partially attenuated in the presence of indomethacin, indicating that the Cai response was mediated in part by cyclooxygenase products of AA. However, the AA-induced Cai response far exceeded that induced by prostaglandins and was mimicked by linoleic acid. We conclude that AA modulates Cai of OLGs via two mechanisms: 1) indirectly via cyclooxygenase pathway and 2) directly via membrane lipid-protein interaction.

Sign in / Sign up

Export Citation Format

Share Document