Protein binds to DNA using a lock and key system
You can think of DNA as a string of letters -- As, Cs, Ts, and Gs -- that together spell out the information needed for cell construction and function. Every cell in your body has the same DNA. Therefore, for cells to assume different roles, they must be able to turn specific genes on and off with precise control. For example, genes that are active in brain cells are different from genes that are active in skin cells.
This is partly achieved by the action of a "DNA binding protein" that locks the human genome at a specific location to turn the gene on or off. Now researchers at the Gladstone Institute, led by Dr. Katherine Pollard, have discovered major discoveries about how these proteins bind to DNA.
Traditionally, scientists have argued that DNA-binding proteins use patterns in the genome codes of As, Cs, Ts, and Gs to direct them to the right place, and that a given protein binds only to a particular sequence of letters. However, many proteins bind several different combinations of letters, and two different proteins recognize the same pattern.
Despite the existence of multiple overlapping patterns, proteins do not seem to be confused about where they should be combined. In a new study published in Cell Systems, Gladstone scientists found that proteins must rely on another clue to know the binding position: the three-dimensional shape of DNA.
"For decades, it's hard to explain how proteins find the right binding sites in DNA, and how they do it in a specific way, and don't bind to the wrong place," Pollard said, he's a Senior researcher and person in charge. Gladstone Institute of Data Science and Biotechnology. "We assume this can be explained by the structural aspects of the genome."
This is because the letter string of DNA is also a physical three-dimensional structure, twisted into a famous double helix shape and wrapped into a microscopic package. In the ladder structure, various distortions, grooves and gaps can be found between the crosspiece and the side. Pollard and her team realized that these changes created a keyhole for protein insertion. If the groove on the protein does not match the groove on the genome, the key will not be suitable.
