Polyamines Mediate Folding of Primordial Hyperacidic Helical Proteins

Abstract

Polyamines are known to mediate diverse biological processes, and specifically to bind and stabilize compact conformations of nucleic acids, acting as chemical chaperones that promote folding by offsetting the repulsive negative charges of the phosphodiester backbone. However, whether and how polyamines modulate the structure and function of proteins remain unclear. In particular, early proteins are thought to have been highly acidic, like nucleic acids, due to a scarcity of basic amino acids in the prebiotic context. Perhaps polyamines, the abiotic synthesis of which is simple, could have served as chemical chaperones for such primordial proteins? We replaced all lysines of an ancestral 60-residue helix-bundle protein with glutamate, resulting in a disordered protein with 21 glutamates in total. Polyamines efficiently induce folding of this hyperacidic protein at submillimolar concentrations, and their potency scaled with the number of amine groups. Compared to cations, polyamines were several orders of magnitude more potent than Na + , while Mg 2+ and Ca 2+ had an effect similar to that of a diamine, inducing folding at approximately seawater concentrations. We propose that (i) polyamines and dications may have had a role in promoting folding of early proteins devoid of basic residues and (ii) coil−helix transitions could be the basis of polyamine regulation in contemporary proteins.

Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids

“…We envision the fixation of the amino acid alphabet as a late event in this sequence of events, as amino acids such as Trp, Tyr, Lys and Arg involve numerous enzymes in their biosynthesis and therefore likely required a DNA-based genome to retain the suite of catalysts necessary to prepare them. An important question that is worth reflecting upon (as we [20,24,104] and others [21–23,26–28,105] have shown) is how proteins managed to complete fairly sophisticated functions in the previous two stages without the full complement of amino acids (see below). The hallmark of this stage is the end of ‘chemical evolution’ as Darwinian biological evolution takes root thanks to the intrinsic stability of information encoded in DNA (compared to RNA), and the high (but not perfect) fidelity of polymerases which create the potential for point mutations, insertions and duplications.…”

Unevolved proteins from modern and prebiotic amino acids manifest distinct structural profiles

“…Where characterized in more detail, assistance of salts, metal ions, or cofactor binding were found to explain the folding properties 15,18,45,47 . In addition, Despotovic et al recently confirmed that folded conformations of a highly acidic 60-residue protein can be induced by positively charged counterions, in case of Mg 2+ the reported concentration corresponding roughly to its concentration in the CFPS reaction (∼10mM) 48 . In parallel, the Hecht group reported that binding of metal ions (with high nanomolar to low micromolar affinity) is a surprisingly frequent property of unevolved sequences and therefore does not require much sequence optimization 49 .…”

“…Where characterized in more detail, assistance of salts, metal ions or cofactor binding were found to explain the folding properties 15,18,42,44 . In addition, Despotovic et al recently confirmed that folded conformations of a highly acidic 60-residue protein can be induced by positively charged counterions, in case of Mg2+ corresponding roughly to its concentration in the CFPS reaction (~10mM) 45 . These studies allow us to hypothesize that the high structural propensity of the 10E alphabet could result from the cation/cofactor-rich environment, where the lack of hydrophobic and electrostatic interactions is compensated by these chemical entities.…”

In vitro evolution reveals primordial RNA-protein interaction mediated by metal cations

“…While previous studies have pointed out that acidic proteins can be soluble and sustain secondary structure information, it has generally been unclear how those proteins can form compact architectures and/or interact with the highly acidic nucleic acids (Doi et al 2011;Tanaka et al 2011;Longo et al 2013;Shibue et al 2018;Newton et al 2019;Solis 2019). A recent study by the Tawfik group suggested that polyamines and divalent cations may have played an important role in promoting the folding of such early proteins (Despotović et al 2020). Similarly, magnesium cations clearly play a special role in the ribosomal structure, a molecular fossil that reports on the earliest interactions between RNA and proteins (Petrov et al 2011).…”