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LIPS specifications

Information


Unique identifier OMICS_13934
Name LIPS
Alternative name LIPid-facing Surface
Interface Web user interface
Restrictions to use None
Input data A multiple sequence alignement of TM helix
Input format FASTA
Output data A residue with helical faces ans an average score for every surface
Programming languages Perl
Computer skills Basic
Stability No
Source code URL http://gila.bioe.uic.edu/lab/lips/lips.txt
Maintained No

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Publication for LIPid-facing Surface

LIPS citations

 (12)
library_books

An allosteric link connecting the lipid protein interface to the gating of the nicotinic acetylcholine receptor

2018
Sci Rep
PMCID: 5832824
PMID: 29497086
DOI: 10.1038/s41598-018-22150-x

[…] pid action are relatively clear in that binding sites in the transmembrane domain (TMD) have been identified, with the bound lipids acting as classic allosteric modulators. In other cases, the entire lipid-facing surface of a TMD may act as an allosteric “site” that is sensitive to the physico-chemical properties of the lipid bilayer, with changes in bilayer physico-chemical properties translated […]

library_books

Discovery and Development of Calcium Channel Blockers

2017
Front Pharmacol
PMCID: 5447095
PMID: 28611661
DOI: 10.3389/fphar.2017.00286

[…] ferent locations of the binding sites of amlodipine and verapamil. Crystallographic analysis showed that amlodipine and other dihydropyridines block the channel pore by interacting with its external, lipid-facing surface but that verapamil interacts with the intracellular side of the selectivity filter and blocks the ion-conducting pathway located in the central cavity of the pore (Tang et al., ). […]

library_books

A mirror code for protein cholesterol interactions in the two leaflets of biological membranes

2016
Sci Rep
PMCID: 4768152
PMID: 26915987
DOI: 10.1038/srep21907

[…] istent with cholesterol promoting the oligomerization of Torpedo γ–TM4. The functional significance of this in the intact receptor remains to be elucidated, but the location of the CARC domain on the lipid-facing surface of the helix may play a role in cholesterol-mediated clustering of the receptor.Overall, our findings show that CARC is a functional cholesterol-binding motif as efficient as CRAC […]

library_books

The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage Gated Potassium Channel

2016
PLoS Comput Biol
PMCID: 4709198
PMID: 26751683
DOI: 10.1371/journal.pcbi.1004704

[…] ions involving hydrophobic residues lining the cavity of the ion pore in the open state []. In contrast, a mutational study proposed a PUFA-interaction site to be located on the VSD, specifically the lipid-facing surface of the extracellular side of TM helices S3 and S4 [].Atomistic MD simulations are designed to monitor structural dynamics of complex environments, such as a membrane protein inser […]

library_books

Mapping the membrane topography of the TH6–TH7 segment of the diphtheria toxin T domain channel

2015
PMCID: 4306713
PMID: 25582482
DOI: 10.1085/jgp.201411326

[…] d 338) react primarily in the open state (), so we might imagine that residues on the right face react in the flicker-closed state. It is not surprising that attaching a positively charged group to a lipid-facing surface of the protein would have strange effects on the channel, such as increasing the conductance and flickering, perhaps indicating a perturbation of the channel structure.Can we reco […]

library_books

Efflux pump proteins in antifungal resistance

2014
Front Pharmacol
PMCID: 4148622
PMID: 25221515
DOI: 10.3389/fphar.2014.00202

[…] ts to be critical based on the fact that almost all TMSs that, upon mutation, abolished resistance to all drugs tested singly or in combinations (Figure ) and were predominantly restricted to the non-lipid-facing surface, consistent with close proximity to the substrate-binding pocket. Lipid bilayer-facing surfaces on each TMS of Cdr1p were identified using the empirical scoring function LIPS (LIP […]

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LIPS institution(s)
Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
LIPS funding source(s)
Supported by the National Science Foundation (CAREER DBI0133856), the National Institute of Health (GM68958), the Office of Naval Research (N000140310329), and the Whitaker Foundation (TF-04-0023).

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