How do DNA binding proteins recognize specific DNA sequences?
Basic Requirements for DNA Binding 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.
Does DNA have beta sheets?
β-Strands. β-Strands paired together to form small β-sheets are also found in sequence-specific DNA interfaces. In these complexes, the β-sheets lie flat within the major groove, where side chains on the exposed surface of the sheet interact with functional groups on the edges of neighboring base pairs.
What motif would you expect when a homodimer forms?
Although each of these proteins has unique features, most bind to DNA as homodimers or heterodimers and recognize DNA through one of a small number of structural motifs. The common motifs include the helix-turn-helix, the homeodomain, the leucine zipper, the helix-loop-helix, and zinc fingers of several types.
How does a regulatory protein with a helix-turn-helix motif recognize a specific DNA sequence?
The helix-turn-helix motif is a DNA-binding motif. The recognition and binding to DNA by helix-turn-helix proteins is done by the two α helices, one occupying the N-terminal end of the motif, the other at the C-terminus.
How do sequence specific DNA-binding proteins recognize their target binding sequences in Watson Crick structure DNA?
DNA-binding proteins recognize their target sites with a number of common binding motifs, such as helix-turn-helix, ββα zinc finger and zipper-type motifs (1). The secondary structure types of amino acids involved in specific protein–DNA binding, however, have not been investigated extensively.
What does beta sheet do?
A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in the formation of the fibrils and protein aggregates observed in amyloidosis, notably Alzheimer’s disease.
Why are beta sheets important?
Beta-sheets consist of expanded strands of polypeptides (beta-strands) linked by a hydrogen bond network and occur widely in proteins. In biological systems, the relevance of beta-sheet associations makes them possible candidates for interference in disorders such as AIDS, tumours, and Alzheimer’s disease.
How does a regulatory protein identify its binding site?
One commonly used approach to identify transcription factor-binding sites is to delineate a group of coregulated genes [e.g., by clustering genes on the basis of their expression profiles (2, 3), or functional annotation] and search for common sequence patterns in their upstream regulatory regions.
What is the purpose of DNA-binding motifs?
The DNA binding proteins have a specific folding pattern which is made of repeated nucleotide sequences called as DNA binding motifs. These motifs permit the binding of DNA binding proteins such as transcription factors to the target sequence. It is composed of recognition region and stabilization region.
What is the difference between helix loop helix and helix turn helix?
The key difference between helix-loop-helix and helix-turn-helix is that helix-loop-helix mediates protein dimerization, whereas helix-turn-helix regulates gene expression through DNA binding. HLH is a protein structural motif that defines one of the largest families of dimerizing transcription factors.
What interactions occur when a protein binds DNA?
Proteins interact with DNA through electrostatic interactions (salt bridges), dipolar interactions (hydrogen bonding, H-bonds), entropic effects (hydrophobic interactions) and dispersion forces (base stacking).
How do transcription factors find their targets?
“Transcription factors differ largely in their ability to scan the genome to find their specific binding sites, and these differences can be predicted by simply looking at how much they bind to mitotic chromosomes,” explained Suter.
What is the role of DNA-binding proteins?
DNA- and RNA-binding proteins (DRBPs) constitute a significant fraction of cellular proteins and have important roles in cells. Their functions include control of transcription and translation, DNA repair, splicing, apoptosis and mediating stress responses.
Why are DNA-binding proteins important?
DNA-binding proteins have a central role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair.
What is a beta turn in proteins?
The Beta Turn Turns generally occur when the protein chain needs to change direction in order to connect two other elements of secondary structure. The most common is the beta turn, in which the change of direction is executed in the space of four residues.
What determines alpha-helix vs beta sheet?
In contrast to the alpha helix, hydrogen bonds in beta sheets form in between N-H groups in the backbone of one strand and C=O. groups in the backbone of the adjacent strands. This is the main difference between Alpha Helix and Beta Pleated Sheet.
What kind of interaction are there in beta sheet structure of protein?
Intermolecular interactions between the hydrogen-bonding edges of β-sheets constitute a fundamental form of biomolecular recognition (like DNA base pairing) and are involved protein quaternary structure, protein-protein interactions, and peptide and protein aggregation.
How do you identify transcription factor binding sites?
Prediction of transcription factor binding sites is generally performed by scanning a DNA sequence of interest with a position weight matrix (PWM) for a transcription factor of interest [6, 7] and various pattern-matching tools have been developed for this purpose.