TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins

Lipid composition in cellular membranes plays an important role in maintaining the structural integrity of cells and in regulating cellular signaling that controls functions of both membrane-anchored and cytoplasmic proteins. ATP-dependent ABC and P4-ATPase lipid transporters, two integral membrane proteins, are known to contribute to lipid translocation across the lipid bilayers on the cellular membranes. In this review, we will highlight current knowledge about the role of cholesterol and phospholipids of cellular membranes in regulating cell signaling and how lipid transporters participate this process.

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Structural and Technological Approach to Reveal the Role of the Lipid Phase in the Formation of Soy Emulsion Gels with Chia Oil

Gels ◽

10.3390/gels7020048 ◽

2021 ◽

Vol 7 (2) ◽

pp. 48

Author(s):

Ana M. Herrero ◽

Claudia Ruiz-Capillas

Keyword(s):

Raman Spectroscopy ◽

Structural Properties ◽

Structural Changes ◽

Protein Secondary Structure ◽

Lipid Phase ◽

Α Helix ◽

Β Sheet ◽

Shed Light ◽

Chia Oil

Considerable attention has been paid to emulsion gels (EGs) in recent years due to their interesting applications in food. The aim of this work is to shed light on the role played by chia oil in the technological and structural properties of EGs made from soy protein isolates (SPI) and alginate. Two systems were studied: oil-free SPI gels (SPI/G) and the corresponding SPI EGs (SPI/EG) that contain chia oil. The proximate composition, technological properties (syneresis, pH, color and texture) and structural properties using Raman spectroscopy were determined for SPI/G and SPI/EG. No noticeable (p > 0.05) syneresis was observed in either sample. The pH values were similar (p > 0.05) for SPI/G and SPI/EG, but their texture and color differed significantly depending on the presence of chia oil. SPI/EG featured significantly lower redness and more lightness and yellowness and exhibited greater puncture and gel strengths than SPI/G. Raman spectroscopy revealed significant changes in the protein secondary structure, i.e., higher (p < 0.05) α-helix and lower (p < 0.05) β-sheet, turn and unordered structures, after the incorporation of chia oil to form the corresponding SPI/EG. Apparently, there is a correlation between these structural changes and the textural modifications observed.

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MexAB-OprM Efflux Pump Interaction with the Peptidoglycan of Escherichia coli and Pseudomonas aeruginosa

International Journal of Molecular Sciences ◽

10.3390/ijms22105328 ◽

2021 ◽

Vol 22 (10) ◽

pp. 5328

Author(s):

Miao Ma ◽

Margaux Lustig ◽

Michèle Salem ◽

Dominique Mengin-Lecreulx ◽

Gilles Phan ◽

...

Keyword(s):

Escherichia Coli ◽

Pseudomonas Aeruginosa ◽

Cell Division ◽

Membrane Proteins ◽

Outer Membrane ◽

Efflux Pump ◽

Gram Negative Bacteria ◽

Gram Negative ◽

Active Efflux

One of the major families of membrane proteins found in prokaryote genome corresponds to the transporters. Among them, the resistance-nodulation-cell division (RND) transporters are highly studied, as being responsible for one of the most problematic mechanisms used by bacteria to resist to antibiotics, i.e., the active efflux of drugs. In Gram-negative bacteria, these proteins are inserted in the inner membrane and form a tripartite assembly with an outer membrane factor and a periplasmic linker in order to cross the two membranes to expulse molecules outside of the cell. A lot of information has been collected to understand the functional mechanism of these pumps, especially with AcrAB-TolC from Escherichia coli, but one missing piece from all the suggested models is the role of peptidoglycan in the assembly. Here, by pull-down experiments with purified peptidoglycans, we precise the MexAB-OprM interaction with the peptidoglycan from Escherichia coli and Pseudomonas aeruginosa, highlighting a role of the peptidoglycan in stabilizing the MexA-OprM complex and also differences between the two Gram-negative bacteria peptidoglycans.

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The Role of Solid Springer in Masonry Vault

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.133-134.349 ◽

2010 ◽

Vol 133-134 ◽

pp. 349-354 ◽

Cited By ~ 1

Author(s):

Vittorio Ceradini ◽

Michele Candela ◽

Roberta Fonti

Keyword(s):

Scientific Research ◽

Evolution Process ◽

Limit Case ◽

Structural Configuration ◽

Structural Role ◽

Different Ages ◽

Building Component ◽

And Function ◽

Technical Rules

During a scientific research, directed to understand the structural role of some particular masonry elements, noticeable in covering structures like vault and dome, we searched the technical rules and function of these elements. We verified that in literature there is no specific documentation about these elements and its mechanic purposes. The study was directed to recognize the most representatives architectures in different ages, and to identify the construction technique’s evolution process of this particular arc-double or thickening of arc that we arrived to identify as a necessary building component to give balance in particular structural configuration. This process put down roots from the roman ancient age, until baroque age, where the most original applications of this regulation were placed. From Pantheon to the limit case of St. Filippo Neri chapel, the covers’ structures springer angle studied was analyzed together with its relation to plan, sections and elevation of all buildings. Therefore, if these elements are well-performed, they follow precise constructive patterns that this article would like to identify and show.

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Specificity and promiscuity in membrane helix interactions

Quarterly Reviews of Biophysics ◽

10.1017/s0033583500004522 ◽

1994 ◽

Vol 27 (2) ◽

pp. 157-218 ◽

Cited By ~ 127

Author(s):

Mark A. Lemmon ◽

Donald M. Engelman

Keyword(s):

Membrane Proteins ◽

Transmembrane Helix ◽

Integral Membrane Proteins ◽

Lipid Packing ◽

Membrane Protein Folding ◽

Membrane Spanning ◽

Α Helix ◽

Prosthetic Groups ◽

Packing Effects ◽

Helix Interactions

The membrane-spanning portions of many integral membrane proteins consist of one or a number of transmembrane α-helices, which are expected to be independently stable on thermodynamic grounds. Side-by-side interactions between these transmembrane α-helices are important in the folding and assembly of such integral membrane proteins and their complexes. In considering the contribution of these helix–helix interactions to membrane protein folding and oligomerization, a distinction between the energetics and specificity should be recognized. A number of contributions to the energetics of transmembrane helix association within the lipid bilayer will be relatively non-specific, including those resulting from charge–charge interactions and lipid–packing effects. Specificity (and part of the energy) in transmembrane α-helix association, however, appears to rely mainly upon a detailed stereochemical fit between sets of dynamically accessible states of particular helices. In some cases, these interactions are mediated in part by prosthetic groups.

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Role of Phosphatidylethanolamine in the Biogenesis of Mitochondrial Outer Membrane Proteins

Journal of Biological Chemistry ◽

10.1074/jbc.m112.442392 ◽

2013 ◽

Vol 288 (23) ◽

pp. 16451-16459 ◽

Cited By ~ 29

Author(s):

Thomas Becker ◽

Susanne E. Horvath ◽

Lena Böttinger ◽

Natalia Gebert ◽

Günther Daum ◽

...

Keyword(s):

Membrane Proteins ◽

Outer Membrane ◽

Outer Membrane Proteins ◽

Proper Function ◽

Mitochondrial Outer Membrane ◽

Tom Complex ◽

Precursor Proteins ◽

Helical Proteins ◽

The Stability

The mitochondrial outer membrane contains proteinaceous machineries for the import and assembly of proteins, including TOM (translocase of the outer membrane) and SAM (sorting and assembly machinery). It has been shown that the dimeric phospholipid cardiolipin is required for the stability of TOM and SAM complexes and thus for the efficient import and assembly of β-barrel proteins and some α-helical proteins of the outer membrane. Here, we report that mitochondria deficient in phosphatidylethanolamine (PE), the second non-bilayer-forming phospholipid, are impaired in the biogenesis of β-barrel proteins, but not of α-helical outer membrane proteins. The stability of TOM and SAM complexes is not disturbed by the lack of PE. By dissecting the import steps of β-barrel proteins, we show that an early import stage involving translocation through the TOM complex is affected. In PE-depleted mitochondria, the TOM complex binds precursor proteins with reduced efficiency. We conclude that PE is required for the proper function of the TOM complex.

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