If protein A "binds stronger" to a DNA fragment than protein B then that
protein A does have a higher affinity and a lower dissociation constant than
the protein B for that DNA fragment.
I actually like the terms "affinity" and "dissociation constant" here
because they seem pretty intuitive to me. If I have an affinity for someone,
I tend to spend time with that someone whenever I encounter them. I randomly
encounter many different people. I have no real affinity for most of these
people, so my random encounter doesn't cause me to spend time "associating"
or hanging around them. If I have a really strong affinity for someone, then
I would hang around that person a lot if I encountered them in a random
waltz down the street. My dissociation constant then would be very low
because we are together more then we are apart. It is quite similar with
proteins and other molecules.
Affinity: How much do two molecules like to stick together? (qualitative)
Dissociation constant: When two molecules are in solution together, what is
the ratio of the two molecules NOT stuck together vs. the two molecules
stuck together? (quantitative)
Please anyone feel free to clarify or correct.
>> My problem is that I havent fully understood what
> the difference is between affinity and
> dissociation constant. When there are two DNA-
> binding proteins and under certain conditions the
> first one binds stronger to its binding site than
> the second one: is the affinity of the first
> protein higher or is the dissociation constant
> lower or both?