Where does the DNA-binding protein bind?
Where does the DNA-binding protein bind?
The protein binds with the a helix in the DNA major groove and the loops in the minor groove, although the latter are not thought to confer specificity. The protein functions as a tetramer with each subunit contacting a separate 5 bp recognition sequence positioned one after another.
Are DNA binding sites for proteins?
In a protein–DNA complex, an amino acid residue in the protein is defined as a binding site if the distance between any atoms of this residue and any atoms of the DNA molecule is less than a specific cutoff value.
What are protein binding sites?
A binding site is a position on a protein that binds to an incoming molecule that is smaller in size comparatively, called ligand. In proteins, binding sites are small pockets on the tertiary structure where ligands bind to it using weak forces (non-covalent bonding).
How do proteins bind to specific DNA sequences?
Proteins recognize a particular sequence by having a surface that is chemically complementary to that of the DNA, forming a series of favorable electrostatic and van der Waals interactions between the protein and the base pairs.
How do proteins bind to proteins?
The selective binding of a protein to another molecule. Many weak bonds are needed to enable a protein to bind tightly to a second molecule, which is called a ligand for the protein. A ligand must therefore fit precisely into a protein’s binding (more…)
Why do proteins bind to the major groove?
Certain proteins bind to DNA to alter its structure or to regulate transcription (copying DNA to RNA) or replication (copying DNA to DNA). It is easier for these DNA binding proteins to interact with the bases (the internal parts of the DNA molecule) on the major groove side because the backbones are not in the way.
Why is DNA bound to basic proteins?
Within chromosomes, DNA is held in complexes with structural proteins. These proteins organize the DNA into a compact structure called chromatin. In eukaryotes, this structure involves DNA binding to a complex of small basic proteins called histones.
What is the role of the P site in translation?
During protein translation, the P-site holds the tRNA which is linked to the growing polypeptide chain. When a stop codon is reached, the peptidyl-tRNA bond of the tRNA located in the P-site is cleaved releasing the newly synthesized protein.
How do you identify a protein binding site?
Guo and Wang identify the binding sites by finding two similar 3D substructures [7]. SiteEngine is a method that recognizes the regions on the surface of one protein that are similar to the binding sites of another. It uses geometric hashing triangles to transfer the input sites into the recognized region [8].
What is the difference between active site and binding site?
Active site is a region on an enzyme to which the substrates of a chemical reaction bind in order to undergo a catalyzed chemical reaction whereas binding site is a region on a protein, DNA or RNA, to which ligands can bind.
How do helix-turn-helix proteins bind to DNA?
In proteins, the helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression.
