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The affinity of an enzyme or a protein transporter indicates the strenght of the binding of substrate/solute. An enzyme with higher affinity binds its substrate more strongly than a counterpart with a lower affinity. Is affinity always a function of the protein structure of enzyme? If the same enzyme in two different species had different affinities for substrate, would that indicate that there were differences in amino acids at the binding sites of the enzyme in the two species?

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    $\begingroup$ I wouldn't say "can bind with more substrate" I would say "binds substrate more strongly" - the answers to your other two questions are yes - affinity is a function of the structure of the enzyme (as well as the shape/structure of the ligand), and yes a difference in affinities in two species indicates there is a difference in amino acids that affects the binding site. Note that it wouldn't necessarily have to be directly at the binding site, just as long as it affects the shape of the binding site. $\endgroup$ – Bryan Krause Apr 30 '17 at 4:32
  • $\begingroup$ Km can most easily be understood as the concentration of ligand that results in half saturation of its target. arxiv.org/pdf/1305.5533.pdf $\endgroup$ – Jeppe Nielsen May 1 '17 at 8:25
  • $\begingroup$ I have edited your question to remove the erroneous description of affinity, corrected in the comment and tightened the wording. I have changed the title to reflect the actual question. I have removed reference to Km because 1) transporters are not enzymes and do not have Kms 2) Km is a parameter that is interpreted in terms of affinity, which may only partially be correct. However as your question is about affinity there is no reason to muddy it with mention of Km. Apologies to @WYSIWYG, but this seems the only way to produce a good question worthy of an answer. $\endgroup$ – David May 1 '17 at 22:28
  • $\begingroup$ @David It depends on how narrowly you define "enzyme", but transporters can indeed be treated identically to enzymes, where the reaction is converting "substance inside" to "substance outside" (or vice versa) rather than making/breaking chemical bonds. Transporters will show the same saturation kinetics as enzymes, and will have kinetic descriptions which have a term equivalent to Km. (Whether you actually call it "Km" is another question.) -- That said, the mention of Km was unnecessary to the question, and I have no issue with its removal. $\endgroup$ – R.M. May 2 '17 at 21:22
  • $\begingroup$ @RM — That same point struck me after writing. But transporters was an odd choice. I'd have thought general ligand binding as for membrane receptors and proteins such as heamoglobin should be included, in which case you would be talking about Kd, I imagine. $\endgroup$ – David May 2 '17 at 21:38
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In a reaction which follows a saturation kinetics, KM is basically the concentration of substrate/ligand at which the rate of the reaction is half of the maximum rate (or the binding sites are half saturated).

The biophysical meaning of KM would depend on the underlying model. For example, in the equilibrium approximation of Michaelis-Menten model, KM is same as dissociation constant (of enzyme and substrate). In the Briggs-Haldane model (quasi steady state approximation), it is slightly complex: KM = (kr + kcat)/kf.

Overall, the thumb rule is that lower the KM faster will the reaction saturate.

Is affinity always a function of the protein structure of enzyme? If someone study same enzyme in two different species and observe that the enzyme has different affinities in two species, then does it indicate that there might by slight difference in key amino-acid component at the binding sites of the enzyme between these two species?

Almost every property of the protein (not just affinity towards a ligand) is because of its chemical composition and structure. Although they are directly involved in binding, the amino acids at binding site are not the sole contributors to the affinity. The other amino acids that are critical for the overall structure of the protein are also important in preserving the function.

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I will add to the answer by @WYSIWYG by turning your question round: “If you changed the amino acids at the binding site, would this affect the affinity of a protein for a ligand*?”

The answer to this is yes, and for an enzyme you can change the substrate specificity entirely, as one can discover from reading this review by Wilson and Agard.

However one should also be aware that changing residues at parts of a protein outside the ligand-binding site can also affect the affinity of binding — see, for example, this paper by Oue et al.

[*This makes the question more general to include other proteins that bind ligands such as membrane receptors and transport proteins such as heamoglobin.]

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