Technology marches on. The influence of all 2^20 = 1,048,576 variants of 5 nucleotides on either side of two consensus sequences for transcription factor binding were (1) synthesized (2) had their dissociation constants (Kd’s) measured. The consensus sequences were for two yeast transcription factors (Pho4 and Cbf1). [ Proc. Natl. Acad. Sci. vol. 115 pp. E3692 – E3702 ’18 ] . The technique is called BET-seq (Binding Energy Topography by sequencing).
What do you think they found?
A ‘large fraction’ of the flanking mutations changed overall binding energies by as much as consensus site mutations. The numbers aren’t huge (only 2.6 kiloCalories/mole). However at 298 Kelvin 25 Centigrade 77 Fahrenheit (where RT = .6) every 1.36 kiloCalories/mole is worth a factor of 10 in the equilibrium constant. So binding can vary by 100 fold even in this range.
The work may explain some ChIP data in which some strips of DNA are occupied despite the lack of a consensus site, with other regions containing consensus sites remaining unoccupied. The authors make the interesting point that submaximal binding sites might be preferred to maximal ones because they’d be easier for the cell to control (notice the anthropomorphism of endowing the cell with consciousness, or natural selection with consciousness). It is very easy to slide into teleological thinking in these matters. Whether or not you like it is a matter of philosophical and/or theological taste.
Pity the poor computational chemist, trying to figure out binding energy to such accuracy with huge molecules like a transcriptional factors and long segments of DNA.
It is also interesting to think what “Molar” means with these monsters. How much does a mole of hemoglobin weigh? 64 kiloGrams more or less. It simply can’t be put into 1000 milliliters of water (which weighs 1 kiloGram). A liter of water contains 1000/18 moles (55.6) moles of water. So solubilizing 1 molecule of hemoglobin would certainly use more than 55 molecules of water. Reality must intrude, but we blithely talk about concentration this way. Does anyone out there know what the maximum achievable concentration of hemoglobin actually is?
Chemiotics II 