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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

Maintainer


This tool is not available anymore.

Publication for LIPid-facing Surface

LIPS in publications

 (12)
PMCID: 5832824
PMID: 29497086
DOI: 10.1038/s41598-018-22150-x

[…] acetylcholine receptor (nachr) is sensitive to its lipid environment. to understand how changes at the lipid-protein interface influence gating, we examined how a mutation at position 418 on the lipid-facing surface of the outer most m4 transmembrane α-helix alters the energetic couplings between m4 and the remainder of the transmembrane domain. human muscle nachr is sensitive to mutations […]

PMCID: 5447095
PMID: 28611661
DOI: 10.3389/fphar.2017.00286

[…] 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., […]

PMCID: 4768152
PMID: 26915987
DOI: 10.1038/srep21907

[…] 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 […]

PMCID: 4709198
PMID: 26751683
DOI: 10.1371/journal.pcbi.1004704

[…] 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 […]

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

[…] 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., […]


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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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