A hydrophobic ratchet entrenches molecular complexes

This will be a bit of a drive-by post because I don’t have the energy to write up a nice summary right now, but I wanted to call attention to a new paper from the Thornton lab that I think will be of interest to some (paging @Rumraket):

A hydrophobic ratchet entrenches molecular complexes


Most proteins assemble into multisubunit complexes1. The persistence of these complexes across evolutionary time is usually explained as the result of natural selection for functional properties that depend on multimerization, such as intersubunit allostery or the capacity to do mechanical work2. In many complexes, however, multimerization does not enable any known function3. An alternative explanation is that multimers could become entrenched if substitutions accumulate that are neutral in multimers but deleterious in monomers; purifying selection would then prevent reversion to the unassembled form, even if assembly per se does not enhance biological function3,4,5,6,7. Here we show that a hydrophobic mutational ratchet systematically entrenches molecular complexes. By applying ancestral protein reconstruction and biochemical assays to the evolution of steroid hormone receptors, we show that an ancient hydrophobic interface, conserved for hundreds of millions of years, is entrenched because exposure of this interface to solvent reduces protein stability and causes aggregation, even though the interface makes no detectable contribution to function. Using structural bioinformatics, we show that a universal mutational propensity drives sites that are buried in multimeric interfaces to accumulate hydrophobic substitutions to levels that are not tolerated in monomers. In a database of hundreds of families of multimers, most show signatures of long-term hydrophobic entrenchment. It is therefore likely that many protein complexes persist because a simple ratchet-like mechanism entrenches them across evolutionary time, even when they are functionally gratuitous.

To understand why multimeric interfaces persist and change over evolutionary time, we studied the evolution of steroid receptors (SRs), a protein family in which dimerization has been maintained for hundreds of millions of years but in which the mechanism of dimerization has diversified. SRs are hormone-activated transcription factors that contain structurally distinct DNA-binding and ligand-binding domains (DBD and LBD, respectively). There are two major phylogenetic classes of SRs (Fig. 1a, b, Extended Data Fig. 1a). One class, the oestrogen receptors (ERs), homodimerize in solution using a large interface in their LBD8,9 and bind palindromic repeats of a particular six-base-pair DNA response element (ERE)10. The other class, called ketosteroid receptors (kSRs) because of the steroidal ligands that activate them, bind to a different palindromic sequence (steroid response element; SRE) via interactions between DBDs11,12. kSR-LBDs are monomeric in solution, and the surface region homologous to the ER dimerization interface binds instead to a C-terminal extension (CTE) on the same LBD, which is absent on ERs (Fig. 1b, c, Extended Data Fig. 1b). Previous work has shown that the ancestral protein from which the two clades arose by gene duplication (AncSR1, more than 500 million years ago) specifically bound oestrogens and non-cooperatively bound EREs; specificity for ketosteroids and SREs, as well as DBD-mediated cooperativity, arose on the branch between AncSR1 and AncSR2, the ancient progenitor of kSRs12,13. We reasoned that by identifying the ancestral and derived forms of the LBD interface and characterizing their effects on function and biophysical properties, we could gain insight into the factors that caused the persistence and modification of this interface across deep history.

Our findings suggest that many molecular complexes are likely to be entrenched by a simple biochemical ratchet: mutational propensity drives sites buried in a multimeric interface to accumulate hydrophobic substitutions to a level that then renders reversion to the ancestral monomeric state deleterious. Complexes in which multimerization makes no direct contribution to function or fitness will therefore be preserved by purifying selection. Other biochemical mechanisms may also entrench multimers, deepening or broadening the effect of hydrophobic enrichment of buried interfaces in causing molecular complexes to persist5.

The lead author, Georg Hochberg, also has a nice twitter thread with a high level overview of the work:


Fascinating. Seems like an excellent example of constructive neutral evolution.

Using structural bioinformatics, we show that a universal mutational propensity drives sites that are buried in multimeric interfaces to accumulate hydrophobic substitutions to levels that are not tolerated in monomers.

Even more fascinating is the idea of an intrinsic mutational bias towards this kind of gratuitous complexity.


Joe Thornton’s collaborations always blow my mind.


Sounds like this could be extrapolated to big complexes like the ribosome, the flagellum, etc.

Of course, the paper itself can be used to explain why haemoglobin evolved from a monomer to homodimer to heterodimer to tetramer.

This could potentially explain alot - that evolution can select for one big complicated machine doing many things rather than lots of little separate ones individually. Then, particular beneficial mutations leading to synergism between the subunits would be particularly beneficial and thus selected for.

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It definitely contributes to the explanations of molecular machines made of many individual protein components. I think in particular the excessive complexity of the spliceosomal complex lends itself very much to this type or process.

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Sounds like directionality to drift…


Yes, fits nicely too with this one:

Notice this:

In emerging but not established ORFs, beneficial fitness effects are associated with a high propensity to encode transmembrane ™ domains. Analyses of genome-wide TM propensities led us to hypothesize that novel adaptive TM peptides may spontaneously emerge when thymine-rich non-genic regions become translated: a “TM-first” model of gene birth.


Our analyses suggest that a simple thymine bias suffices to generate a diverse reservoir of novel TM peptides (Fig. 5a–c), and that incipient proto-genes with TM domains are more likely to increase fitness than proto-genes without TM domains (Fig. 4).

Seems there’s an intrinsic mutational bias towards hydrophobic proteins.

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I was about to post this article again when Discourse informed it was already here! :sweat_smile:

Would it be fair to say a lot of “Irreducible Complexity” evolves simply because it biochemically favored, and not because it has anything to do with function?


Yep, it would.