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The tilting angle refers to the angle relative to the membrane. The shear number (S) is the number of amino acid residues found in each β strands. Strand number (n) is the amount of β strands in the porin, and barrel radius (R) refers to the radius of the opening of the porin. These parameters are related via the following formulas:
The pelB leader sequence is a sequence of amino acids which, when attached to a protein, directs the protein to the bacterial periplasm, where the sequence is removed by a signal peptidase. [1] Specifically, pelB refers to pectate lyase B of Erwinia carotovora CE. The leader sequence consists of the 22 N-terminal amino acid residues.
The amino acid composition of the porin β-strands are unique in that polar and non-polar residues alternate along them. This means that the non-polar residues face outwards so as to interact with the non-polar lipid membrane, whereas the polar residues face inwards into the center of the β-barrel to form the aqueous channel.
The two amino acid residues are linked through a peptide bond. As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins.
Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. The genetic code is a set of three-nucleotide sets called codons and each three-nucleotide combination designates an amino acid, for example AUG (adenine–uracil–guanine) is the code for methionine.
For shear number in barrels, displacement is measured in units of amino acid residues. The determination of shear number requires the assumption that each amino acid in one strand of a beta sheet is adjacent to just one amino acid in the neighboring strand (this assumption may not hold if, for example, a beta bulge is present). [12]
The flagellin domains are numbered from the helical core (D0/D1) to the outside (D2, ...); when viewed from the amino-acid sequence, D0/D1 appears on the two termini. Flagellin-like structural proteins are found in other portions of the flagellum, such as the hook (flgE; P75937 ), the rod at the base, and the cap at the top.
Bacterial Leucine Transporter (LeuT) is a bundled twelve alpha helix protein which belongs to the family of transporters that shuttle amino acids in and out of bacterial cells. Specialized in small hydrophobic amino acids such as leucine and alanine , this transporter is powered by the gradient of sodium ions that is normally maintained by ...