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Is Bh%e2%82%83 Polar Or Nonpolar
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Interplay Between Oxygen And Fe–s Cluster Biogenesis: Insights From The Suf Pathway
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By Sonia Khemaissa Sonia Khemaissa Scilit Preprints.org Google Scholar, Sandrine Sagan Sandrine Sagan Scilit Preprints.org Google Scholar and Astrid Walrant Astrid Walrant Scilit Preprints.org Google Scholar *
Received: 27 July 2021 / Revised: 23 August 2021 / Accepted: 24 August 2021 / Published: 27 August 2021
Journal Of Applied Polymer Science
Tryptophan is an aromatic amino acid with unique physicochemical properties. It is often found in membrane proteins, especially at the water/bilayer interface. It plays a role in the stabilization, attachment and organization of membrane proteins in lipid bilayers. It has hydrophobic properties, but can enter into many types of interactions, such as π-cations or hydrogen bonds. In this review, we provide an overview of the role of tryptophan in membrane proteins and a more detailed description of the non-covalent interactions it can make with membrane partners.
Among naturally encoded eukaryotic amino acids, tryptophan (Trp) is unique in its physicochemical properties. It is considered an aromatic residue similar to tyrosine (Tyr), phenylalanine (Phe) or histidine (His), but it is the only amino acid with two rings in its side chain, i.e. the indole part of the benzene ring melts. for the pyrrole ring, making it the largest encoded amino acid in the natural series.
According to several different hydrophobic/hydrophilic scales that have been developed by different research groups over the years to classify amino acids, Trp is considered more or less hydrophobic. The nitrogen in the indole ring may participate in hydrogen bonding, which may facilitate protein solubilization. The large quadrupole allows it to enter strong π–π or π–cation interactions. Also, Trp has the same dipole moment as Tyr, but not Phe. All these special physicochemical properties make Trp unique in terms of biological function and protein localization. In this review, we outline the importance of these unique Trp properties in membrane proteins and help to understand their location and function.
Analysis of amino acid distribution in proteins shows that Trp is found in most transmembrane proteins, accounting for 3.3% of total amino acids, except for 1.2% of soluble protein .
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In these transmembrane proteins, Trp has a strong preference for bilayer interactions, as first demonstrated by Jacobs and White using neutron diffraction . Since then, other techniques have been used to determine the location of Trp, including X-ray diffraction , nuclear magnetic resonance (NMR) , fluorescence spectroscopy , and molecular simulation . All these studies point in the same direction: Trp is located at the lipid/water interface. In fact, Trp is not the only residue found at the interface, aromatic residues usually occupy this position in transmembrane proteins of α helix and β structures, which are called the “aromatic belt”  (Figure 1).
Interestingly, the aromatic residues are not randomly distributed at the interface. Indeed, aromatic residues are often found at the lipid-extracellular interface . This observation has been reported in the case of photosynthetic reaction centers where Trp is located mainly in the periplasmic side . Another study showed this specifically for 29 integral proteins and highlighted the fact that Trp is found in non-cytoplasmic interactions for transmembrane helical α proteins according to a sequence-based method. The same study shows that this residue is more common in the α helical structure than in the β structure . However, this trend is not true for all proteins. For example, in the transmembrane segment of human type I membrane proteins, Trp is located at both ends of the hydrophobic domain, while Tyr is located only at the C-terminus and Phe is located in the hydrophobic domain and region. Tyr position .
Trp is located at the interface and more precisely in the region of the acyl carbonyl group of the lipid layer, as shown by the chemical shift of the signal given to the choline group in the presence of Trp [9, 10] .
Another study shows that Trp is also located in the glycerol region and in the hydrophobic core of the lipid bilayer, according to
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H NMR study. The authors suggest that the location of Trp in the choline region may be controlled mainly by cation-π interactions, while other types of interactions may occur in the glycerol region, such as van der Waals interaction, dipolar interaction, entropic contribution, or hydrogen. binding. [10, 11]. The interfacial localization of Trp allows it to make contact with choline moieties, as mentioned above, but may also involve contact with other molecules present in its environment, such as water, which binds to the -hydrogen. Protein residues, such as Arg and Lys, are located close to the phosphate moieties because deeper positions in the hydrophobic core are unfavorable and lead to specific lipid associations . Trp can positively interact with cationic residues through cation-π bonds.
Trp has a preference for hydrophilic regions over hydrophobic bases . If we focus on its orientation in the two layers, the benzene part of the indole prefers the hydrophobic core, while the pyrrole part shows the more hydrophilic part of the lipid layer [8, 14]
Molecular simulations were performed for indole in the POPC phospholipid bilayer and confirmed this trend, showing the presence of three weak Trp binding sites, in the choline region, the glycerol region and the base, the hydrophobic one, offering different types of interactions depending on the nature. the binding site . All these connections will be further explored in the second part of the manuscript.
Trp is an essential residue involved in thermal stability , stabilization of tertiary and quaternary structures [16, 17] and in protein processes in general . It also plays an important role in protein binding sites [19, 20, 21, 22, 23].
Chem32a Lab_polar & Nonpolar_06oct13
Focusing on membrane proteins, Trp is often found at the helix-helix transmembrane interface, where it may be involved in protein folding . This residue is located at both ends of the α-helices, whereas it is located only at one end of the β-loop structure in the OmpF porin [ 25 , 26 ]. In addition, it was observed that in 3.2% of cases it was associated with the symmetric part of the membrane protein, confirming the idea of the important contribution of the residues in the protein folding process. Furthermore, in membrane proteins Trp interacts with residues distant from it, suggesting its effect in stabilizing the tertiary structure. However, unlike the case of the α-helix structure, its contribution to the free energy of the unfolded state appears to be limited to β-barrel membrane proteins . In fact, this stabilizing effect is highly dependent on the Trp position and the environment. In fact, mutation of one Trp of OmpX from Tyr or Phe changes the folding kinetics and stability of the protein, while the same mutation at other positions has no effect  . Some studies have shown the important contribution of Trp to the binding and stability of proteins when located at the interface [28, 29], while other studies have emphasized its importance when placed in the middle of the layer . This ambivalent nature is due to the complexity of the layered structure, which affects the active contribution of each amino acid to protein stability, meaning that the role of Trp depends on its sequence . Stabilizing effects can occur through hydrogen bonding between Trp residues and lipid carbons, depending on their position in the interface.
Although Trp contributes to the stability of membrane proteins, it does not appear to be required for protein insertion into the membrane. Indeed, in a study that mutated the Trp residue to Ala, it was shown that these mutations lead to a decrease in