I was reading Errett C. Hobbsa 's paper, titled "Conserved small protein associates with the multidrug efflux pump AcrB and differentially affects antibiotic resistance" .
In this paper the author described the affinity of AcrB and AcrZ could effect the drug efflux pump's substrates recognition. The author proved this idea by experiments.
In his supporting information of this paper, the author provided a alignment between AA sequences of AcrB and AcrZ. They found the similarity between AcrZ and AcrB in TM2 and TM3 region of AcrB. TM2 and TM3 are the binding interfaces of AcrZ and AcrB.
So my question is that the amino acid sequences similarity related to the affinity of proteins?
It is plausible to the paper's logic. I am trying to find the resources of this method, but I failed to find the further supporting information.
I think that this is a complex question. While AA composition certainly plays a large role in dictating affinity, I don't think that is the whole story. An example of AA dictating affinity would be substituting a hydrophilic AA into a hydrophobic pocket that is the binding site of another protein. Although both the WT and mutant protein would be highly similar in AA content, the presence of a hydrophilic AA in the binding pocket would most likely abolish or mitigate the binding affinity (assuming that it is a hydrophobic interaction).
In addition, there is growing evidence that the entropy of a protein (in the form of side chain dynamics) also contributes to binding affinity. There is a paper in JACS by someone I did a postdoc with that found that AA identify is less conserved compared to dynamic characteristics of the side-chains in the context of protein-protein interactions.
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