Table of Contents
What are periplasmic binding proteins?
Periplasmic binding proteins (PBPs) are bacterial receptors that exhibit dramatic conformational changes upon ligand binding. These proteins mediate a wide variety of fundamental processes including transport, chemotaxis, and quorum sensing.
What increases binding affinity?
The smaller the KD value, the greater the binding affinity of the ligand for its target. The larger the KD value, the more weakly the target molecule and ligand are attracted to and bind to one another.
What is the first protein that binds to DNA?
In eukaryotes, this structure involves DNA binding to a complex of small basic proteins called histones. In prokaryotes, multiple types of proteins are involved. The histones form a disk-shaped complex called a nucleosome, which contains two complete turns of double-stranded DNA wrapped around its surface.
What is the role of binding protein in ABC transporter?
ATP-binding cassette (ABC) transporters, although being ubiquitous in biology, often feature a subunit that is limited primarily to bacteria and archaea. This subunit, the substrate-binding protein (SBP), is a key determinant of the substrate specificity and high affinity of ABC uptake systems in these organisms.
What is binding affinity proteins?
Binding affinity is the strength of the binding interaction between a single biomolecule (e.g. protein or DNA) to its ligand/binding partner (e.g. drug or inhibitor).
How is the leucine zipper formed and what is its function?
Leucine zipper is created by the dimerization of two specific alpha helix monomers bound to DNA. The leucine zipper is formed by amphipathic interaction between two ZIP domains. The ZIP domain is found in the alpha-helix of each monomer, and contains leucines, or leucine-like amino acids.
What is ATP-binding cassette protein?
ATP-binding cassette (ABC) transporters are a large superfamily of membrane proteins with diverse functions (Holland et al. 2003). They convert the energy gained from ATP hydrolysis into trans-bilayer movement of substrates either into the cytoplasm (import) or out of the cytoplasm (export).
How do leucine zippers bind to DNA?
What is leucine zipper structure?
A heptad repeat of leucine residues, leucine zipper (ZIP), is an important sequence motif facilitating protein–protein interactions. ZIP forms an amphiphilic α helical structure, in which two residues that are separated by seven residues in sequence are located at nearly the same molecular surface in an α helix.
How does a leucine zipper bind to DNA?
On dimerization, the leucine-zipper a helices form a parallel-coiled coil based on hydrophobic interfacial side-chain packing (55). The dimerization brings the DNA-binding surface to the positions appropriate for contacting DNA in a scissor-grip mode (56) or in an induced helical fork mode (57).
How do ATP-binding cassettes work?
What is the structure of L-leucine-binding protein?
The L-leucine-binding protein structure is, as expected, very similar to the Leu/Ile/Val-binding protein structure; both are in the unliganded conformation with the cleft between the two domains wide open and easily accessible.
Oscar Millet, in Advances in Protein Chemistry and Structural Biology, 2013 Periplasmic binding proteins (PBPs) constitute a large family of receptors that recognize a plethora of small molecules and ions in gram-negative bacteria (Quiocho & Ledvina, 1996 ).
What is the sequence identity of amino acid binding proteins?
The two amino acid-binding proteins have 80% sequence identity and, although both crystallize in the same space group, they have very different unit cell dimensions. The rotation function yielded one significant peak, which subsequently led to a single self-consistent translation function solution.
What is the mechanism of drug uptake in bacteria?
Mechanisms of drug uptake in bacteria utilize outer membrane (OM) porins, periplasmic binding proteins, and inner membrane (IM) pumps (7, 21). Relatively selective channels may be used by some antibiotics (e.g., imipenem), and nutrient transporters may be used by others (e.g., aminoglycosides).